Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 182 of 230
Found at i:54625438 original size:108 final size:107
Alignment explanation
Indices: 54625343--54625550 Score: 240
Period size: 108 Copynumber: 1.9 Consensus size: 107
54625333 TAATACATTT
*
54625343 ATGA-GAATA-AAGAAAAATATATATAGAAATTATAAAAATATGGGTAGAAAGTATAATATATAT
1 ATGATGAATATAAG-AAAATATATATAGAAATTAT-AAAATATGGATAGAAAGTAT-A-ATATAT
* * * * *
54625406 ATACGTACATATATATGTAAGTTAATAAATATAGACCATAAAGATG
62 ATACGTACATATATATATAAGGTAACAAATATATACAATAAAGATG
* * *** * *
54625452 ATGATTGCATATATGTGTATATATATATAAATTATAAAATATGTATAGAAAGTATAATATATATA
1 ATGA-TGAATATAAGAAAATATATATAGAAATTATAAAATATGGATAGAAAGTATAATATATATA
54625517 CGTACATATATATATAAGGTAACAAATATATACA
65 CGTACATATATATATAAGGTAACAAATATATACA
54625551 TCATAAACAT
Statistics
Matches: 83, Mismatches: 13, Indels: 7
0.81 0.13 0.07
Matches are distributed among these distances:
108 38 0.46
109 5 0.06
110 18 0.22
111 20 0.24
112 2 0.02
ACGTcount: A:0.51, C:0.04, G:0.12, T:0.33
Consensus pattern (107 bp):
ATGATGAATATAAGAAAATATATATAGAAATTATAAAATATGGATAGAAAGTATAATATATATAC
GTACATATATATATAAGGTAACAAATATATACAATAAAGATG
Found at i:54625498 original size:20 final size:20
Alignment explanation
Indices: 54625470--54625516 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
54625460 ATATATGTGT
* *
54625470 ATATATATATAAATTATAAA
1 ATATATATAGAAAGTATAAA
* *
54625490 ATATGTATAGAAAGTATAAT
1 ATATATATAGAAAGTATAAA
54625510 ATATATA
1 ATATATA
54625517 CGTACATATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.38
Consensus pattern (20 bp):
ATATATATAGAAAGTATAAA
Found at i:54625548 original size:110 final size:111
Alignment explanation
Indices: 54625359--54625575 Score: 287
Period size: 110 Copynumber: 2.0 Consensus size: 111
54625349 ATAAAGAAAA
* *
54625359 ATATATATAGAAATTATAAAAATATGGGTAGAAAGTATAATATATATATACGTACATATATATGT
1 ATATATATAGAAATTATAAAAATATGGATAGAAAGTATAATATATATATACGTACATATATATAT
* * * * * * *
54625424 AAGTTAATAAATATAGACCATAAAGATGATGATTGCATATATGTGT
66 AAGGTAAAAAATATACACCATAAACATAATAATTACATATATGTGT
* *
54625470 ATATATATATAAATTAT-AAAATATGTATAGAAAGTAT-A-ATATATATACGTACATATATATAT
1 ATATATATAGAAATTATAAAAATATGGATAGAAAGTATAATATATATATACGTACATATATATAT
*
54625532 AAGGTAACAAATATATACATCATAAACATAATAATTACATATAT
66 AAGGTAA-AAA-ATATACACCATAAACATAATAATTACATATAT
54625576 AAGCTTAAAA
Statistics
Matches: 92, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
108 29 0.32
109 3 0.03
110 44 0.48
111 16 0.17
ACGTcount: A:0.50, C:0.06, G:0.10, T:0.35
Consensus pattern (111 bp):
ATATATATAGAAATTATAAAAATATGGATAGAAAGTATAATATATATATACGTACATATATATAT
AAGGTAAAAAATATACACCATAAACATAATAATTACATATATGTGT
Found at i:54626985 original size:44 final size:44
Alignment explanation
Indices: 54626937--54627235 Score: 222
Period size: 44 Copynumber: 6.9 Consensus size: 44
54626927 AATCTAGGGT
* *
54626937 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATCAGC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCTCAGC
* * **
54626981 TTTAATTTGCTCCACTGCAACTTCAGGGAAATAAGATT-TGCCATT
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCT--CAGC
* * *
54627026 TTTAGTCT-CCCTCACTGCAACTTCA-GGAGGATAAGACTTGCTTA-C
1 TTTAATCTGCTC-CACTGCAACTTCAGGGA-GATAAGA-TT-CTCAGC
* * *
54627071 -TTAGTCTGCTCCACTACAACTTCAGGGAGATAAGA--CT-AGA
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCTCAGC
* * ** * * * *
54627111 TGTGATCTGCT-CTTTGCAACTTCAGAGAGGTAAGA-TCTGAGAT
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCTCAG-C
* * * * **
54627154 TTTAATCCGCTCCACTGCAACTTCAGGAAGATAGGATTGTTGGC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCTCAGC
*
54627198 TTTAATCTGCTCCACTGTAACTTCAGGGAGATAAGATT
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
54627236 TGCCATCTTC
Statistics
Matches: 199, Mismatches: 40, Indels: 32
0.73 0.15 0.12
Matches are distributed among these distances:
39 1 0.01
40 21 0.11
41 9 0.05
42 2 0.01
43 9 0.05
44 118 0.59
45 35 0.18
46 3 0.02
48 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.31
Consensus pattern (44 bp):
TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCTCAGC
Found at i:54627303 original size:44 final size:44
Alignment explanation
Indices: 54627255--54627566 Score: 132
Period size: 44 Copynumber: 7.1 Consensus size: 44
54627245 CAGCCTGCCT
54627255 CACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTC
1 CACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTC
* * * *
54627299 CACTATTG-TCTAGGGA-AGT-AGAATTACTG---GCTTCAATGTACTC
1 CACTACTGCT-TAGGGAGA-TAAG-A-T-CTGAAATCTTCAATCTATTC
** * * ** * *
54627342 CACTGTAAC--CACAGGGAGGTAAAATCTGCCATCTTCGATCTACTC
1 CAC--T-ACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTC
54627387 CACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTC
1 CACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTC
** ** * * *
54627431 CACTGTTGCCCAGGGA-AGT-AGATTTACTG--GT-TTCAATGTACTC
1 CACTACTGCTTAGGGAGA-TAAGA--T-CTGAAATCTTCAATCTATTC
** * * ** * *
54627474 CACTGTAAC--CACAGGGAGGTAAAATCTGCCATCTTCGATCTGTTC
1 CAC--T-ACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTC
*
54627519 CACTACTGCTTAGGGAGATAAGATCTAAAATCTTCAATCTATTC
1 CACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTC
54627563 CACT
1 CACT
54627567 GTTGCCCAGG
Statistics
Matches: 192, Mismatches: 46, Indels: 60
0.64 0.15 0.20
Matches are distributed among these distances:
42 10 0.05
43 39 0.20
44 104 0.54
45 32 0.17
46 7 0.04
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (44 bp):
CACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTC
Found at i:54627348 original size:132 final size:132
Alignment explanation
Indices: 54627207--54628570 Score: 2221
Period size: 132 Copynumber: 10.3 Consensus size: 132
54627197 CTTTAATCTG
** * * * *
54627207 CTCCACTGTAACTTCAGGGAGATAAGATTTGCCATCTTC-AGCCTGC-CTCACTACTGCTTAGGG
1 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGA-TCTGCTC-CACTACTGCTTAGGG
* *
54627270 AGATAAGATCTGAAATCTTCAATCTATTCCACTATTGTCTAGGGAAGTAGAATTACTGGCTTCAA
64 AGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAA
54627335 TGTA
129 TGTA
*
54627339 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTACTCCACTACTGCTTAGGGAG
1 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAG
* * *
54627404 ATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGATTTACTGGTTTCAATG
66 ATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATG
54627469 TA
131 TA
*
54627471 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTGTTCCACTACTGCTTAGGGAG
1 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAG
* *
54627536 ATAAGATCTAAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACTGGCTTCAATG
66 ATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATG
54627601 TA
131 TA
**
54627603 CTCCACTGTAACCACAGGGAGGTAAAATCCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAG
1 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAG
* * *
54627668 ATAATACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTA-AAGTTACTAGCTTCAAT
66 ATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAA-TTACTGGCTTCAAT
54627732 GTA
130 GTA
*
54627735 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCTTCTTCGATCTGCTCCACTACTGCTTAGGGAG
1 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAG
* *
54627800 ATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGTGAAGTAGAATTACTGGCTTCAATG
66 ATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATG
54627865 TA
131 TA
*
54627867 CTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAG
1 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAG
* * * *
54627932 ATAAGATCTAAAATCTTCAATCTATTCCGCTGTTGTTCAGGGAAGTAGAATTACTGACTTCAATG
66 ATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATG
54627997 TA
131 TA
54627999 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAG
1 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAG
* * * * *
54628064 ATAAGACCTGAAATCTTCAATCTATCCCGCTGTTGTCCAGAGAAGTAGAGTTACTGGCTTCAATG
66 ATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATG
54628129 TA
131 TA
54628131 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAG
1 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAG
*
54628196 ATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATG
66 ATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATG
54628261 TA
131 TA
* * * *
54628263 CTCCACTATAACCATAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTACTTAGGGAG
1 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAG
* *
54628328 ATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTAGTTTCAATG
66 ATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATG
54628393 TA
131 TA
* * *
54628395 CTCCACTATAACCACAGGGAGGTAAAATCCGCCATTTTCGATCTGCTCCACTACTGCTTAGGGAG
1 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAG
* * * * * *
54628460 ATAAGATCTGAAATCTTTAATCTATTCCACCGTTGTTCGGGGAAGTAGAATTACTGGTTTCAATA
66 ATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATG
54628525 TA
131 TA
* *
54628527 CTCCACTGTAACCACAGGGAGGTATAATCCGCCATCTTCGATCT
1 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCT
54628571 ACTTCGCTGT
Statistics
Matches: 1158, Mismatches: 70, Indels: 8
0.94 0.06 0.01
Matches are distributed among these distances:
131 2 0.00
132 1152 0.99
133 4 0.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (132 bp):
CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAG
ATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATG
TA
Found at i:54633810 original size:98 final size:98
Alignment explanation
Indices: 54633639--54633835 Score: 376
Period size: 98 Copynumber: 2.0 Consensus size: 98
54633629 GTGCAATAAA
*
54633639 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
54633704 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
54633737 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
*
54633802 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
54633835 A
1 A
54633836 TTATTTTTAA
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
98 97 1.00
ACGTcount: A:0.38, C:0.25, G:0.10, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
Found at i:54634389 original size:21 final size:22
Alignment explanation
Indices: 54634365--54634416 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 22
54634355 ATAAAGAAAT
*
54634365 ATATATATAGAAATTATAA-AA
1 ATATATATAGAAAGTATAATAA
*** *
54634386 ATATGGGTAGAAAGTATAATAT
1 ATATATATAGAAAGTATAATAA
54634408 ATATATATA
1 ATATATATA
54634417 CGTACATATA
Statistics
Matches: 22, Mismatches: 8, Indels: 1
0.71 0.26 0.03
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.35
Consensus pattern (22 bp):
ATATATATAGAAAGTATAATAA
Found at i:54634506 original size:20 final size:20
Alignment explanation
Indices: 54634478--54634524 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
54634468 ATATATGTGT
* *
54634478 ATATATATATAAATTATAAA
1 ATATATATAGAAAGTATAAA
* *
54634498 ATATGTATAGAAAGTATAAT
1 ATATATATAGAAAGTATAAA
54634518 ATATATA
1 ATATATA
54634525 CGTACATATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.38
Consensus pattern (20 bp):
ATATATATAGAAAGTATAAA
Found at i:54634517 original size:56 final size:55
Alignment explanation
Indices: 54634363--54634522 Score: 137
Period size: 56 Copynumber: 2.8 Consensus size: 55
54634353 GAATAAAGAA
* * *
54634363 ATATATATATAGAAATTATAAAAATATGGGTAGAAAGTATAATATATATATATACGT
1 ATATATATATATAAATTAT-AAAATAT-GATAGAAAGTATAATATATACATATACGT
* * * * * * *
54634420 ACATATATATGTAAGTTA-ATAAATATAGACCATAAAG-ATAATGAT-TGCATATATGT
1 ATATATATATATAAATTATA-AAATAT-GA-TAGAAAGTATAAT-ATATACATATACGT
*
54634476 GTATATATATATAAATTATAAAATATGTATAGAAAGTATAATATATA
1 ATATATATATATAAATTATAAAATATG-ATAGAAAGTATAATATATA
54634523 TACGTACATA
Statistics
Matches: 78, Mismatches: 18, Indels: 15
0.70 0.16 0.14
Matches are distributed among these distances:
55 9 0.12
56 47 0.60
57 22 0.28
ACGTcount: A:0.50, C:0.03, G:0.11, T:0.36
Consensus pattern (55 bp):
ATATATATATATAAATTATAAAATATGATAGAAAGTATAATATATACATATACGT
Found at i:54634843 original size:20 final size:21
Alignment explanation
Indices: 54634820--54634858 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
54634810 TTAAAGGGCA
*
54634820 AATTTAAAAGATAA-AAAAAT
1 AATTGAAAAGATAATAAAAAT
*
54634840 AATTGAAAATATAATAAAA
1 AATTGAAAAGATAATAAAA
54634859 GACAGAAGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (21 bp):
AATTGAAAAGATAATAAAAAT
Found at i:54651867 original size:63 final size:63
Alignment explanation
Indices: 54651788--54651915 Score: 256
Period size: 63 Copynumber: 2.0 Consensus size: 63
54651778 TTTTTGAAAC
54651788 ACCAAATTAATATATATTATAATTTCAAAATGTTATACAGGTGAATTTAATAGAAGAATTTTA
1 ACCAAATTAATATATATTATAATTTCAAAATGTTATACAGGTGAATTTAATAGAAGAATTTTA
54651851 ACCAAATTAATATATATTATAATTTCAAAATGTTATACAGGTGAATTTAATAGAAGAATTTTA
1 ACCAAATTAATATATATTATAATTTCAAAATGTTATACAGGTGAATTTAATAGAAGAATTTTA
54651914 AC
1 AC
54651916 GGCGGCAATA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.38
Consensus pattern (63 bp):
ACCAAATTAATATATATTATAATTTCAAAATGTTATACAGGTGAATTTAATAGAAGAATTTTA
Found at i:54652013 original size:34 final size:33
Alignment explanation
Indices: 54651949--54652014 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 33
54651939 TCTAAATCCA
*
54651949 AAAAGTAGAAGGATTAAATTCCTAAAATAAAAAT
1 AAAAGTAGAA-GATTAAATTCCAAAAATAAAAAT
*
54651983 AAAAGTAGAA-ATTAAATTCCAAATATATAAAA
1 AAAAGTAGAAGATTAAATTCCAAAAATA-AAAA
54652015 GACATAGAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 15 0.52
33 4 0.14
34 10 0.34
ACGTcount: A:0.61, C:0.06, G:0.09, T:0.24
Consensus pattern (33 bp):
AAAAGTAGAAGATTAAATTCCAAAAATAAAAAT
Found at i:54653624 original size:51 final size:51
Alignment explanation
Indices: 54653548--54653650 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
54653538 AGATGAACAT
54653548 ATGAATTCTTGGAAGTTTTAACAACAACAATAAATAATAAATGCATTCGTG
1 ATGAATTCTTGGAAGTTTTAACAACAACAATAAATAATAAATGCATTCGTG
*
54653599 ATGAATTCTTGGAAGTTTTAACAACAACAATAAATAATAAATGCATTTGTG
1 ATGAATTCTTGGAAGTTTTAACAACAACAATAAATAATAAATGCATTCGTG
54653650 A
1 A
54653651 GAAACAGACA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.32
Consensus pattern (51 bp):
ATGAATTCTTGGAAGTTTTAACAACAACAATAAATAATAAATGCATTCGTG
Found at i:54653761 original size:39 final size:39
Alignment explanation
Indices: 54653717--54653794 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
54653707 TAAAAGTATA
54653717 ATAAAAGTTATAATTAAAATTTAGAAGCAATGAGTTTTG
1 ATAAAAGTTATAATTAAAATTTAGAAGCAATGAGTTTTG
54653756 ATAAAAGTTATAATTAAAATTTAGAAGCAATGAGTTTTG
1 ATAAAAGTTATAATTAAAATTTAGAAGCAATGAGTTTTG
54653795 TTTTGGGTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.46, C:0.03, G:0.15, T:0.36
Consensus pattern (39 bp):
ATAAAAGTTATAATTAAAATTTAGAAGCAATGAGTTTTG
Found at i:54661319 original size:16 final size:18
Alignment explanation
Indices: 54661292--54661325 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
54661282 TAGAATTGAG
54661292 TTGAGAAAATT-ATTTAA
1 TTGAGAAAATTAATTTAA
54661309 TTGAG-AAATTAATTTAA
1 TTGAGAAAATTAATTTAA
54661326 GATATTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (18 bp):
TTGAGAAAATTAATTTAA
Found at i:54669142 original size:19 final size:19
Alignment explanation
Indices: 54669106--54669142 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
54669096 TTGATGTAAA
*
54669106 TAAAATATATTAAAATAGG
1 TAAAATATAATAAAATAGG
*
54669125 TAAAATATAATAACATAG
1 TAAAATATAATAAAATAG
54669143 TTTTTAGAAG
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:0.59, C:0.03, G:0.08, T:0.30
Consensus pattern (19 bp):
TAAAATATAATAAAATAGG
Found at i:54669508 original size:4 final size:4
Alignment explanation
Indices: 54669499--54669539 Score: 73
Period size: 4 Copynumber: 10.2 Consensus size: 4
54669489 TAATAGAGCT
*
54669499 AGTA AGTA AGCA AGTA AGTA AGTA AGTA AGTA AGTA AGTA A
1 AGTA AGTA AGTA AGTA AGTA AGTA AGTA AGTA AGTA AGTA A
54669540 TAATAATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.51, C:0.02, G:0.24, T:0.22
Consensus pattern (4 bp):
AGTA
Found at i:54669583 original size:3 final size:3
Alignment explanation
Indices: 54669537--54669569 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
54669527 AGTAAGTAAG
54669537 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
54669570 AAGGCTAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:54669615 original size:22 final size:22
Alignment explanation
Indices: 54669574--54669615 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
54669564 TAATAAAAGG
* *
54669574 CTAATAATAAAATATTAATAAA
1 CTAATAATAAAAAATCAATAAA
*
54669596 CTAATATTAAAAAATCAATA
1 CTAATAATAAAAAATCAATA
54669616 GAAAACAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (22 bp):
CTAATAATAAAAAATCAATAAA
Found at i:54670066 original size:9 final size:9
Alignment explanation
Indices: 54670052--54670095 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 9
54670042 TTTCAAAACG
54670052 AAAAGAAAA
1 AAAAGAAAA
54670061 AAAAGAAAA
1 AAAAGAAAA
54670070 GAAAAGAAAA
1 -AAAAGAAAA
54670080 ATAAA-AAAA
1 A-AAAGAAAA
*
54670089 ACAAGAA
1 AAAAGAA
54670096 CCCAAATGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
8 2 0.06
9 17 0.55
10 12 0.39
ACGTcount: A:0.84, C:0.02, G:0.11, T:0.02
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:54670068 original size:14 final size:14
Alignment explanation
Indices: 54670046--54670079 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
54670036 TTCATTTTTC
*
54670046 AAAACGAAAAGAAA
1 AAAAAGAAAAGAAA
54670060 AAAAAGAAAAGAAA
1 AAAAAGAAAAGAAA
54670074 AGAAAA
1 A-AAAA
54670080 ATAAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAGAAA
Found at i:54670069 original size:5 final size:5
Alignment explanation
Indices: 54670046--54670079 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
54670036 TTCATTTTTC
54670046 AAAACG AAAAG AAAA- AAAAG AAAAG AAAAG AAAA
1 AAAA-G AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
54670080 ATAAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.15
5 19 0.70
6 4 0.15
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:54670088 original size:19 final size:18
Alignment explanation
Indices: 54670046--54670088 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
54670036 TTCATTTTTC
*
54670046 AAAACGAAAAGAAAAAAA
1 AAAAAGAAAAGAAAAAAA
54670064 AGAAAAGAAAAGAAAAATAA
1 A-AAAAGAAAAGAAAAA-AA
54670084 AAAAA
1 AAAAA
54670089 ACAAGAACCC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 18 0.82
20 3 0.14
ACGTcount: A:0.84, C:0.02, G:0.12, T:0.02
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAAAA
Found at i:54670250 original size:16 final size:16
Alignment explanation
Indices: 54670226--54670256 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54670216 TTCTCTTTTT
*
54670226 TATTTTTATATATATA
1 TATTCTTATATATATA
54670242 TATTCTTATATATAT
1 TATTCTTATATATAT
54670257 GATTAATAGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTCTTATATATATA
Found at i:54671571 original size:129 final size:129
Alignment explanation
Indices: 54671277--54672671 Score: 2097
Period size: 129 Copynumber: 10.8 Consensus size: 129
54671267 ACTACAACTT
* * * * ** *
54671277 CAGGGAGATAGGA-TTATCGGCTTCAATCTGCTTCCTTACTCTTGAAGATAAGATTCACTGTCAT
1 CAGGGATATAGGACTTGT-GGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTC-T
* *
54671341 T-AATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTT-CCAACCTATTCCA-TCGCTG
64 TCGATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACT-GCTG
54671403 AC
128 AC
* * *
54671405 CAGGGATATAGGACTTGTGGCTCAAATCTGATTCCTTACACTTGAAGATAAGATTTGCCATCTTC
1 CAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTCTTC
* * * *
54671470 GATCTGCTCCGCTATTGCTTAAGGAGGCAAGA-CGGTTAATTTCCCAACCTATTCTACTGCTGAC
66 GATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTG-TAATTTCCCAACCTATTCCACTGCTGAC
*
54671534 CAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTC
1 CAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTCTTC
*
54671599 GATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTACTGAC
66 GATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGAC
* * *
54671663 CAGTGATATAGGACTTGTGGCTTAAATCTGCTTCTTTACACTTGAAGATAAGATTCGCCGTCTTC
1 CAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTCTTC
* * **
54671728 GATCTGCTCCGCTACTGCTTAGGGATACAAGATCTGTAATTT-CTGACCTATTCCACTGCTGAC
66 GATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGAC
* ** * **
54671791 CAGAGAGGTAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCACCGTCTTC
1 CAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTCTTC
* ** *
54671856 GATCTGCTCCACTACTT-CTTAGGGAGACAAGATCTGTAATTT-CTGACCTATTCCACTACTGAC
66 GATCTGCTCCGCTA-TTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGAC
* *
54671919 CAGGGAAATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTTGCCGTCTTC
1 CAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTCTTC
* *
54671984 GATCTGCTCCGCTATTGCTTAGAGAGACAAGATCTGTAATTTCCCATCCTATTCCACTGCTGAC
66 GATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGAC
* * *
54672048 C-GGAGAAATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTTGCCGTATT
1 CAGG-GATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTCTT
*
54672112 CGATCTGCTCCGCTATTGCTTAGAGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGAC
65 CGATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGAC
* * **
54672177 CAGAGAAATAGGACTTGTGGCTTAAATCTGCTTCCTTATTCTTGAAGATAAGATTTGCCGTCTTC
1 CAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTCTTC
54672242 GATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGAC
66 GATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGAC
* **
54672306 CAGGGATATAGGACTTGTAGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCACCTTC
1 CAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTCTTC
* *
54672371 GATCTGCTCCGCTATTGCTTAGGAAGACAAGATCTGTAATTTCCCAACCTATTTCACTGCTGAC
66 GATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGAC
* *
54672435 CAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTCAAGATAAGATTTGCCGCCTTC
1 CAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTCTTC
* * *
54672500 GATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCTAACCTATTCTACCGCTGAC
66 GATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGAC
* * * *
54672564 CAGGGATATAGGACTTGTCGCTTAAATCTGCTTCCTTACACTTGAAAATAAGATTTGCAGCCTTC
1 CAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTCTTC
* * *
54672629 GATCTGTTCCGCTACTGCTTAGGGAGACAAGATTTGTAATTTC
66 GATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTC
54672672 TCTGATCTGT
Statistics
Matches: 1173, Mismatches: 83, Indels: 21
0.92 0.06 0.02
Matches are distributed among these distances:
127 6 0.01
128 315 0.27
129 848 0.72
130 4 0.00
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (129 bp):
CAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTCTTC
GATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGAC
Found at i:54672209 original size:514 final size:515
Alignment explanation
Indices: 54671281--54672671 Score: 2141
Period size: 514 Copynumber: 2.7 Consensus size: 515
54671271 CAACTTCAGG
* * * *
54671281 GAGATAGGA-TTATCGGCTTCAATCTGCTTCCTTACTCTTGAAGATAAGATTCACTGTCATT-AA
1 GAGATAGGACTTGT-GGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCACCGTC-TTCGA
*
54671344 TCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCA-TCGCTGACCAG
64 TCTGCTCCGCTACTTCTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACT-GCTGACCAG
* * *
54671408 GGATATAGGACTTGTGGCTCAAATCTGATTCCTTACACTTGAAGATAAGATTTGCCATCTTCGAT
128 GGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTCTTCGAT
* *
54671473 CTGCTCCGCTATTGCTTA-AGGAGGCAAGA-CGGTTAATTTCCCAACCTATTCTACTGCTGACCA
193 CTGCTCCGCTATTGCTTAGA-GAGACAAGATCTG-TAATTTCCCAACCTATTCTACTGCTGACCA
*
54671536 GGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGA
256 GGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTCTTCGA
54671601 TCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTACTGACCAG
321 TCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTACTGACCAG
* * *
54671666 TGATATAGGACTTGTGGCTTAAATCTGCTTCTTTACACTTGAAGATAAGATTCGCCGTCTTCGAT
386 AGAAATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGAT
* **
54671731 CTGCTCCGCTACTGCTTAGGGATACAAGATCTGTAATTT-CTGACCTATTCCACTGCTGACCAGA
451 CTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGA
*
54671795 GAGGTAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCACCGTCTTCGATC
1 GAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCACCGTCTTCGATC
* ** *
54671860 TGCTCCACTACTTCTTAGGGAGACAAGATCTGTAATTTCTGACCTATTCCACTACTGACCAGGGA
66 TGCTCCGCTACTTCTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCAGGGA
* *
54671925 AATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTTGCCGTCTTCGATCTG
131 TATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTCTTCGATCTG
* *
54671990 CTCCGCTATTGCTTAGAGAGACAAGATCTGTAATTTCCCATCCTATTCCACTGCTGACC-GGAGA
196 CTCCGCTATTGCTTAGAGAGACAAGATCTGTAATTTCCCAACCTATTCTACTGCTGACCAGG-GA
* * *
54672054 AATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTTGCCGTATTCGATCTG
260 TATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTCTTCGATCTG
* *
54672119 CTCCGCTATTGCTTAGAGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGAGAA
325 CTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTACTGACCAGAGAA
** *
54672184 ATAGGACTTGTGGCTTAAATCTGCTTCCTTATTCTTGAAGATAAGATTTGCCGTCTTCGATCTGC
390 ATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGC
* *
54672249 TCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGG
455 TCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGA
* * * ** **
54672310 GATATAGGACTTGTAGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCACCTTCGATC
1 GAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCACCGTCTTCGATC
* *
54672375 TGCTCCGCTA-TTGCTTAGGAAGACAAGATCTGTAATTTCCCAACCTATTTCACTGCTGACCAGG
66 TGCTCCGCTACTT-CTTAGGGAGACAAGATCTGTAATTT-CCAACCTATTCCACTGCTGACCAGG
* *
54672439 GATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTCAAGATAAGATTTGCCGCCTTCGATC
129 GATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTCTTCGATC
* * *
54672504 TGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCTAACCTATTCTACCGCTGACCAGGG
194 TGCTCCGCTATTGCTTAGAGAGACAAGATCTGTAATTTCCCAACCTATTCTACTGCTGACCAGGG
* * * *
54672569 ATATAGGACTTGTCGCTTAAATCTGCTTCCTTACACTTGAAAATAAGATTTGCAGCCTTCGATCT
259 ATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTCTTCGATCT
* * *
54672634 GTTCCGCTACTGCTTAGGGAGACAAGATTTGTAATTTC
324 GCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTC
54672672 TCTGATCTGT
Statistics
Matches: 797, Mismatches: 70, Indels: 18
0.90 0.08 0.02
Matches are distributed among these distances:
513 4 0.01
514 441 0.55
515 119 0.15
516 231 0.29
517 2 0.00
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (515 bp):
GAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCACCGTCTTCGATC
TGCTCCGCTACTTCTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCAGGGA
TATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTCTTCGATCTG
CTCCGCTATTGCTTAGAGAGACAAGATCTGTAATTTCCCAACCTATTCTACTGCTGACCAGGGAT
ATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTCTTCGATCTGC
TCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTACTGACCAGAGAAA
TAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCT
CCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGA
Found at i:54673874 original size:23 final size:23
Alignment explanation
Indices: 54673831--54673874 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
54673821 TAATAAAAGG
* *
54673831 CTAATAATAAAAATATTAATAAA
1 CTAATAATAAAAAAATCAATAAA
*
54673854 CTAATATTAAAAAAATCAATA
1 CTAATAATAAAAAAATCAATA
54673875 GAAAACAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.30
Consensus pattern (23 bp):
CTAATAATAAAAAAATCAATAAA
Found at i:54674343 original size:18 final size:17
Alignment explanation
Indices: 54674303--54674347 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
54674293 TTAATTTTTC
*
54674303 AAAACGAAAAGAAAAAA
1 AAAAAGAAAAGAAAAAA
54674320 AGAAAAGAAAAGAAAAATA
1 A-AAAAGAAAAGAAAAA-A
54674339 AAAAA-AAAA
1 AAAAAGAAAA
54674348 CAAGAATCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 5 0.20
18 18 0.72
19 2 0.08
ACGTcount: A:0.84, C:0.02, G:0.11, T:0.02
Consensus pattern (17 bp):
AAAAAGAAAAGAAAAAA
Found at i:54675358 original size:44 final size:40
Alignment explanation
Indices: 54675251--54675542 Score: 134
Period size: 44 Copynumber: 6.8 Consensus size: 40
54675241 ATTTGCTATC
54675251 TTTAATCTGCTCCACTACAACTTCAGGAAGATAAGACTTGA
1 TTTAATCTGCTCCACTACAACTTCAGG-AGATAAGACTTGA
* * * * * *
54675292 TGTGATCTACTCTATTACAACTTCAGAGAGATAAGATCTATTA
1 TTTAATCTGCTCCACTACAACTTCAG-GAGATAAGA-CT-TGA
* * * *
54675335 TTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGC
1 -TTTAATCTGCTCCACTACAACTTCA-GGAGATAAGACT-T--GA
* * * *
54675380 TTCAATCTGCTCCACTGCAACCTCAGGGAGATAAGATTTGACA
1 TTTAATCTGCTCCACTACAACTTCA-GGAGATAAGACTTG--A
* * * * * * * *
54675423 TATTCAATCTACCCCACTGCAACCTCAGGGGGATACGACCTGC
1 T-TT-AATCTGCTCCACTACAACTTCA-GGAGATAAGACTTGA
*** * * * *
54675466 TGCGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTATTA
1 TTTAATCTGCTCCACTACAACTTCAG-GAGATAAGA-CT-TGA
*
54675509 CTTTAATCCGCTCCACTACAACTTCAGGGAGATA
1 -TTTAATCTGCTCCACTACAACTTCA-GGAGATA
54675543 GGATTATCGG
Statistics
Matches: 187, Mismatches: 48, Indels: 29
0.71 0.18 0.11
Matches are distributed among these distances:
40 1 0.01
41 55 0.29
42 4 0.02
43 9 0.05
44 85 0.45
45 33 0.18
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (40 bp):
TTTAATCTGCTCCACTACAACTTCAGGAGATAAGACTTGA
Found at i:54675827 original size:129 final size:129
Alignment explanation
Indices: 54675533--54676927 Score: 2097
Period size: 129 Copynumber: 10.8 Consensus size: 129
54675523 ACTACAACTT
* * * * ** *
54675533 CAGGGAGATAGGA-TTATCGGCTTCAATCTGCTTCCTTACTCTTGAAGATAAGATTCACTGTCAT
1 CAGGGATATAGGACTTGT-GGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTC-T
* *
54675597 T-AATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTT-CCAACCTATTCCA-TCGCTG
64 TCGATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACT-GCTG
54675659 AC
128 AC
* * *
54675661 CAGGGATATAGGACTTGTGGCTCAAATCTGATTCCTTACACTTGAAGATAAGATTTGCCATCTTC
1 CAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTCTTC
* * *
54675726 GATCTGCTCCGCTATTGCTTAAGGAGACAAGA-CGGTTAATTTCCCAACCTATTCTACTGCTGAC
66 GATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTG-TAATTTCCCAACCTATTCCACTGCTGAC
* *
54675790 CAGGGATATAGGAGTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTC
1 CAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTCTTC
* *
54675855 GATCTGCTCCACTATTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTACTGAC
66 GATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGAC
* * *
54675919 CAGTGATATAGGACTTGTGGCTTAAATCTGCTTCTTTACACTTGAAGATAAGATTCGCCGTCTTC
1 CAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTCTTC
* * *
54675984 GATCTGCTCCGCTACTGCTTAGGGATACAAGATCTGTAATTT-CCGACCTATTCCACTGCTGAC
66 GATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGAC
* ** * **
54676047 CAGAGAGGTAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCACCGTCTTC
1 CAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTCTTC
* **
54676112 GATCTGCTCCACTACTT-CTTAGGGAGACAAGATCTGTAATTT-CTGACCTATTCCACTGCTGAC
66 GATCTGCTCCGCTA-TTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGAC
* *
54676175 CAGGGAAATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTTGCCGTCTTC
1 CAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTCTTC
* *
54676240 GATCTGCTCCGCTATTGCTTAGAGAGACAAGATCTGTAATTTCCCATCCTATTCCACTGCTGAC
66 GATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGAC
* * *
54676304 C-GGAGAAATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTTGCCGTATT
1 CAGG-GATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTCTT
*
54676368 CGATCTGCTCCGCTATTGCTTAGAGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGAC
65 CGATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGAC
* * **
54676433 CAGAGAAATAGGACTTGTGGCTTAAATCTGCTTCCTTATTCTTGAAGATAAGATTTGCCGTCTTC
1 CAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTCTTC
54676498 GATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGAC
66 GATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGAC
* **
54676562 CAGGGATATAGGACTTGTAGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCACCTTC
1 CAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTCTTC
* *
54676627 GATCTGCTCCGCTATTGCTTAGGGAAACAAGATCTGTAATTTCCCAACCTATTTCACTGCTGAC
66 GATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGAC
* **
54676691 CAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTCAAGATAAGATTTGCCCCCTTC
1 CAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTCTTC
* * *
54676756 GATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCTAACCTATTCTACCGCTGAC
66 GATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGAC
* * * *
54676820 CAGGGATATAGGACTTGTCGCTTAAATCTGCTTCCTTACACTTGAAAATAAGATTTGCAGCCTTC
1 CAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTCTTC
* * *
54676885 GATCTGTTCCGCTACTGCTTAGGGAGACAAGATTTGTAATTTC
66 GATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTC
54676928 TCTGATCTGT
Statistics
Matches: 1172, Mismatches: 84, Indels: 21
0.92 0.07 0.02
Matches are distributed among these distances:
127 6 0.01
128 317 0.27
129 845 0.72
130 4 0.00
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (129 bp):
CAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTCTTC
GATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGAC
Found at i:54676465 original size:514 final size:515
Alignment explanation
Indices: 54675537--54676927 Score: 2141
Period size: 514 Copynumber: 2.7 Consensus size: 515
54675527 CAACTTCAGG
* * * *
54675537 GAGATAGGA-TTATCGGCTTCAATCTGCTTCCTTACTCTTGAAGATAAGATTCACTGTCATT-AA
1 GAGATAGGACTTGT-GGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCACCGTC-TTCGA
*
54675600 TCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCA-TCGCTGACCAG
64 TCTGCTCCGCTACTTCTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACT-GCTGACCAG
* *
54675664 GGATATAGGACTTGTGGCTCAAATCTGATTCCTTACACTTGAAGATAAGATTTGCCATCTTCGAT
128 GGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCATCTTCGAT
*
54675729 CTGCTCCGCTATTGCTTA-AGGAGACAAGA-CGGTTAATTTCCCAACCTATTCTACTGCTGACCA
193 CTGCTCCGCTATTGCTTAGA-GAGACAAGATCTG-TAATTTCCCAACCTATTCTACTGCTGACCA
* *
54675792 GGGATATAGGAGTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGA
256 GGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTCTTCGA
*
54675857 TCTGCTCCACTATTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTACTGACCAG
321 TCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTACTGACCAG
* * *
54675922 TGATATAGGACTTGTGGCTTAAATCTGCTTCTTTACACTTGAAGATAAGATTCGCCGTCTTCGAT
386 AGAAATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGAT
* *
54675987 CTGCTCCGCTACTGCTTAGGGATACAAGATCTGTAATTT-CCGACCTATTCCACTGCTGACCAGA
451 CTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGA
*
54676051 GAGGTAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCACCGTCTTCGATC
1 GAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCACCGTCTTCGATC
* **
54676116 TGCTCCACTACTTCTTAGGGAGACAAGATCTGTAATTTCTGACCTATTCCACTGCTGACCAGGGA
66 TGCTCCGCTACTTCTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCAGGGA
* * *
54676181 AATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTTGCCGTCTTCGATCTG
131 TATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCATCTTCGATCTG
* *
54676246 CTCCGCTATTGCTTAGAGAGACAAGATCTGTAATTTCCCATCCTATTCCACTGCTGACC-GGAGA
196 CTCCGCTATTGCTTAGAGAGACAAGATCTGTAATTTCCCAACCTATTCTACTGCTGACCAGG-GA
* * *
54676310 AATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTTGCCGTATTCGATCTG
260 TATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTCTTCGATCTG
* *
54676375 CTCCGCTATTGCTTAGAGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGAGAA
325 CTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTACTGACCAGAGAA
** *
54676440 ATAGGACTTGTGGCTTAAATCTGCTTCCTTATTCTTGAAGATAAGATTTGCCGTCTTCGATCTGC
390 ATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGC
* *
54676505 TCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGG
455 TCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGA
* * * ** **
54676566 GATATAGGACTTGTAGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCACCTTCGATC
1 GAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCACCGTCTTCGATC
* *
54676631 TGCTCCGCTA-TTGCTTAGGGAAACAAGATCTGTAATTTCCCAACCTATTTCACTGCTGACCAGG
66 TGCTCCGCTACTT-CTTAGGGAGACAAGATCTGTAATTT-CCAACCTATTCCACTGCTGACCAGG
* **
54676695 GATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTCAAGATAAGATTTGCCCCCTTCGATC
129 GATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCATCTTCGATC
* * *
54676760 TGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCTAACCTATTCTACCGCTGACCAGGG
194 TGCTCCGCTATTGCTTAGAGAGACAAGATCTGTAATTTCCCAACCTATTCTACTGCTGACCAGGG
* * * *
54676825 ATATAGGACTTGTCGCTTAAATCTGCTTCCTTACACTTGAAAATAAGATTTGCAGCCTTCGATCT
259 ATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTCTTCGATCT
* * *
54676890 GTTCCGCTACTGCTTAGGGAGACAAGATTTGTAATTTC
324 GCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTC
54676928 TCTGATCTGT
Statistics
Matches: 798, Mismatches: 69, Indels: 18
0.90 0.08 0.02
Matches are distributed among these distances:
513 4 0.01
514 441 0.55
515 120 0.15
516 231 0.29
517 2 0.00
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (515 bp):
GAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCACCGTCTTCGATC
TGCTCCGCTACTTCTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCAGGGA
TATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCATCTTCGATCTG
CTCCGCTATTGCTTAGAGAGACAAGATCTGTAATTTCCCAACCTATTCTACTGCTGACCAGGGAT
ATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCGTCTTCGATCTGC
TCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTACTGACCAGAGAAA
TAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCT
CCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGA
Found at i:54683427 original size:19 final size:19
Alignment explanation
Indices: 54683391--54683427 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
54683381 TTGATGTAAA
*
54683391 TAAAATATATTAAAATAGG
1 TAAAATATAATAAAATAGG
*
54683410 TAAAATATAATAACATAG
1 TAAAATATAATAAAATAG
54683428 TTTTTAGAAG
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:0.59, C:0.03, G:0.08, T:0.30
Consensus pattern (19 bp):
TAAAATATAATAAAATAGG
Found at i:54683795 original size:4 final size:4
Alignment explanation
Indices: 54683786--54683830 Score: 81
Period size: 4 Copynumber: 11.2 Consensus size: 4
54683776 TAATAGAGCT
*
54683786 AGTA AGTA AGCA AGTA AGTA AGTA AGTA AGTA AGTA AGTA AGTA A
1 AGTA AGTA AGTA AGTA AGTA AGTA AGTA AGTA AGTA AGTA AGTA A
54683831 TAATAATAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.51, C:0.02, G:0.24, T:0.22
Consensus pattern (4 bp):
AGTA
Found at i:54683880 original size:3 final size:3
Alignment explanation
Indices: 54683828--54683866 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
54683818 AGTAAGTAAG
54683828 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
54683867 AAGGCTAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:54683892 original size:12 final size:12
Alignment explanation
Indices: 54683832--54683906 Score: 71
Period size: 12 Copynumber: 6.2 Consensus size: 12
54683822 AGTAAGTAAT
*
54683832 AATAATAATAAT
1 AATAATAATAAA
*
54683844 AATAATAATAAT
1 AATAATAATAAA
54683856 AATAATAATAAA
1 AATAATAATAAA
*
54683868 AGGCTAATAATAAA
1 A--ATAATAATAAA
*
54683882 AATATTAAT-AA
1 AATAATAATAAA
* *
54683893 ACTAATATTAAA
1 AATAATAATAAA
54683905 AA
1 AA
54683907 ATCAATAGAA
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
11 8 0.15
12 33 0.63
14 11 0.21
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (12 bp):
AATAATAATAAA
Found at i:54684331 original size:16 final size:15
Alignment explanation
Indices: 54684308--54684344 Score: 65
Period size: 16 Copynumber: 2.4 Consensus size: 15
54684298 AAACAAAAAG
54684308 AAAAAAATAAAATAA
1 AAAAAAATAAAATAA
54684323 AAGAAAAATAAAATAA
1 AA-AAAAATAAAATAA
54684339 AAAAAA
1 AAAAAA
54684345 CAAGAACCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.86, C:0.00, G:0.03, T:0.11
Consensus pattern (15 bp):
AAAAAAATAAAATAA
Found at i:54694052 original size:19 final size:18
Alignment explanation
Indices: 54694017--54694052 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
54694007 AATATAAAAT
*
54694017 TATTATTTTATATTATAA
1 TATTATTTTATAATATAA
54694035 TATTATTTGTATAATATA
1 TATTATTT-TATAATATA
54694053 TTAACTCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (18 bp):
TATTATTTTATAATATAA
Found at i:54700360 original size:13 final size:13
Alignment explanation
Indices: 54700342--54700405 Score: 83
Period size: 13 Copynumber: 4.9 Consensus size: 13
54700332 AGTTCTTCAT
54700342 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
54700355 TGCTTTTAAAAAG
1 TGCTTTTGAAAAG
* *
54700368 TGCTGTGGAAAAG
1 TGCTTTTGAAAAG
*
54700381 TGCTGTTGAAAAG
1 TGCTTTTGAAAAG
*
54700394 TGGTTTTGAAAA
1 TGCTTTTGAAAA
54700406 TTTTTAGTGT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 44 1.00
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.34
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:54701039 original size:12 final size:12
Alignment explanation
Indices: 54701022--54701047 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
54701012 GTTGTTTGAT
54701022 TCACCGTCATCA
1 TCACCGTCATCA
54701034 TCACCGTCATCA
1 TCACCGTCATCA
54701046 TC
1 TC
54701048 GTCGTTGTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.42, G:0.08, T:0.27
Consensus pattern (12 bp):
TCACCGTCATCA
Found at i:54702584 original size:72 final size:72
Alignment explanation
Indices: 54702457--54702767 Score: 498
Period size: 72 Copynumber: 4.3 Consensus size: 72
54702447 AAAATCATAT
** ** *
54702457 ATAAACAACTATTGATAAAACTATTTTA-GTATAAATAAGTAAAACATAAATTCAATATCCAAAA
1 ATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCAATATCCAAAA
54702521 ACCAAAC
66 ACCAAAC
* *
54702528 ATAAACAACTATTAATAAAACTAGATTACACATAAATAAGTAGAATATAAATTCAATATCCAAAA
1 ATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCAATATCCAAAA
54702593 ACCAAAC
66 ACCAAAC
* *
54702600 ATAAACAACTATTAATAAAACTAGATTACACATAAATAAGTAGAATATAAATTCAATATCCAAAA
1 ATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCAATATCCAAAA
54702665 ACCAAAC
66 ACCAAAC
* *
54702672 ATAAACAACCATTGATAAAACTAGATTACACATAAATAAGTATAACATAAATTCAATATCCAAAA
1 ATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCAATATCCAAAA
*
54702737 ACTAAAC
66 ACCAAAC
*
54702744 ATAAATAACTATTGATAAAACTAG
1 ATAAACAACTATTGATAAAACTAG
54702768 TTTAGCATTG
Statistics
Matches: 225, Mismatches: 14, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
71 25 0.11
72 200 0.89
ACGTcount: A:0.56, C:0.15, G:0.05, T:0.25
Consensus pattern (72 bp):
ATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCAATATCCAAAA
ACCAAAC
Found at i:54706062 original size:12 final size:12
Alignment explanation
Indices: 54706045--54706069 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54706035 CTGGGGATCT
54706045 AGCAATCAGTAA
1 AGCAATCAGTAA
54706057 AGCAATCAGTAA
1 AGCAATCAGTAA
54706069 A
1 A
54706070 CTCTAAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (12 bp):
AGCAATCAGTAA
Found at i:54706213 original size:13 final size:13
Alignment explanation
Indices: 54706195--54706235 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
54706185 AGTAAAGCAA
54706195 AGCAGAGCAAAGC
1 AGCAGAGCAAAGC
54706208 AGCAGAGGCATAA--
1 AGCAGA-GCA-AAGC
54706221 AGCAGAGCAAAGC
1 AGCAGAGCAAAGC
54706234 AG
1 AG
54706236 TAAAGAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
11 2 0.08
12 3 0.12
13 14 0.58
14 3 0.12
15 2 0.08
ACGTcount: A:0.46, C:0.20, G:0.32, T:0.02
Consensus pattern (13 bp):
AGCAGAGCAAAGC
Found at i:54708664 original size:3 final size:3
Alignment explanation
Indices: 54708658--54708710 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
54708648 GAGTATAATA
54708658 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
54708706 ATG AT
1 ATG AT
54708711 TAAGAAGTAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:54709665 original size:53 final size:53
Alignment explanation
Indices: 54709607--54709712 Score: 203
Period size: 53 Copynumber: 2.0 Consensus size: 53
54709597 TAAGAGAGAA
54709607 TGTGATTTGTATGGTGAAAAGTACTAAAATTAAGAAATGAATATGTAATCTAC
1 TGTGATTTGTATGGTGAAAAGTACTAAAATTAAGAAATGAATATGTAATCTAC
*
54709660 TGTGATTTGTATGGTGAAAAGTACTAAGATTAAGAAATGAATATGTAATCTAC
1 TGTGATTTGTATGGTGAAAAGTACTAAAATTAAGAAATGAATATGTAATCTAC
54709713 ACATAAACTT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.41, C:0.06, G:0.20, T:0.34
Consensus pattern (53 bp):
TGTGATTTGTATGGTGAAAAGTACTAAAATTAAGAAATGAATATGTAATCTAC
Found at i:54718461 original size:50 final size:51
Alignment explanation
Indices: 54718285--54718471 Score: 216
Period size: 51 Copynumber: 3.7 Consensus size: 51
54718275 TATAAACACG
* * * * *
54718285 TGTGTAGTACTAAGTGCAGGCTACTACATGTATC-GATAGATAATGATCACA
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAAAGCT-TTGATCACA
* * * * * * *
54718336 TGTGCAGTAGTATGTGCAGGCTACTATGTGTACCGGAAGGCTTTGGTCACG
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAAAGCTTTGATCACA
*
54718387 TGTGTAGTACTATGTGCAGGCTACTACGTGAATCGGAAAG-TTTGATCACA
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAAAGCTTTGATCACA
* *
54718437 TGTGTAGTACTATGTGAAGACTACTACGTGTATCG
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTATCG
54718472 AATGATAATA
Statistics
Matches: 112, Mismatches: 23, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
50 40 0.36
51 68 0.61
52 4 0.04
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (51 bp):
TGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAAAGCTTTGATCACA
Found at i:54721961 original size:27 final size:27
Alignment explanation
Indices: 54721931--54721982 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
54721921 CGAAATTCAT
54721931 ACTTAAATTA-TAAAATAATTAATTTAC
1 ACTT-AATTATTAAAATAATTAATTTAC
* *
54721958 ACTTAATTATTAACATATTTAATTT
1 ACTTAATTATTAAAATAATTAATTT
54721983 TAATTATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (27 bp):
ACTTAATTATTAAAATAATTAATTTAC
Found at i:54723746 original size:79 final size:82
Alignment explanation
Indices: 54723635--54723819 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
54723625 GCTACTCGTT
* * *
54723635 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
54723698 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
54723715 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
54723778 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
54723795 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
54723820 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:54723819 original size:40 final size:40
Alignment explanation
Indices: 54723616--54723819 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
54723606 CGGAATTTAA
** *
54723616 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
54723656 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
54723696 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
54723735 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
54723775 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
54723815 CCGGA
1 CCGGA
54723820 CATCATTCAA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 92 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:54731661 original size:79 final size:82
Alignment explanation
Indices: 54731550--54731734 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
54731540 GCTACTCGTT
* * *
54731550 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
54731613 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
54731630 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
54731693 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
54731710 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
54731735 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:54731734 original size:40 final size:40
Alignment explanation
Indices: 54731531--54731734 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
54731521 CGGAATTTAA
** *
54731531 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
54731571 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
54731611 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
54731650 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
54731690 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
54731730 CCGGA
1 CCGGA
54731735 CATCATTCAA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 92 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:54736202 original size:44 final size:44
Alignment explanation
Indices: 54736139--54736229 Score: 130
Period size: 44 Copynumber: 2.1 Consensus size: 44
54736129 AACTCTGTTT
* *
54736139 TTAGTTTACCATTTAAACTCTAATTAGTGTATG-TTATTTTAATA
1 TTAGTTTACCACTTAAACTCTAATTAGTGTA-GATTATTATAATA
* *
54736183 TTAGTTTCCCACTTAAACTCTGATTAGTGTAGATTATTATAATA
1 TTAGTTTACCACTTAAACTCTAATTAGTGTAGATTATTATAATA
54736227 TTA
1 TTA
54736230 TTTGACCTAC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
43 1 0.02
44 41 0.98
ACGTcount: A:0.32, C:0.11, G:0.10, T:0.47
Consensus pattern (44 bp):
TTAGTTTACCACTTAAACTCTAATTAGTGTAGATTATTATAATA
Found at i:54752248 original size:33 final size:33
Alignment explanation
Indices: 54752206--54752360 Score: 119
Period size: 33 Copynumber: 4.6 Consensus size: 33
54752196 AAGATACGGT
54752206 GGAATCAGCACTTAGCAACCACCAATGATTCGG
1 GGAATCAGCACTTAGCAACCACCAATGATTCGG
54752239 GGAATCAGCACTTAGCAACC-CC------TCGGG
1 GGAATCAGCACTTAGCAACCACCAATGATTC-GG
*
54752266 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATAT-GG
1 GGAATCAGCACTTAGCAA-CCAC--CA-A--T--GAT-TCGG
* *
54752307 TGGAATCAGTACTTAGCAACCACCAATGAGTCGG
1 -GGAATCAGCACTTAGCAACCACCAATGATTCGG
*
54752341 GGAATCAACACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
54752361 CCCTTTATAT
Statistics
Matches: 98, Mismatches: 5, Indels: 38
0.70 0.04 0.27
Matches are distributed among these distances:
26 2 0.02
27 20 0.20
28 2 0.02
29 1 0.01
31 1 0.01
32 2 0.02
33 39 0.40
34 4 0.04
36 1 0.01
38 1 0.01
39 2 0.02
41 5 0.05
42 17 0.17
43 1 0.01
ACGTcount: A:0.32, C:0.28, G:0.21, T:0.19
Consensus pattern (33 bp):
GGAATCAGCACTTAGCAACCACCAATGATTCGG
Found at i:54752344 original size:102 final size:102
Alignment explanation
Indices: 54752159--54752362 Score: 336
Period size: 102 Copynumber: 2.0 Consensus size: 102
54752149 TTATCCGTTA
* * * *
54752159 TCGGTGGATTCAGCATTTAGCAACCCCTTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAA
1 TCGGGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAA
* *
54752224 CCACCAATGATTCGGGGAATCAGCACTTAGCAACCCC
66 CCACCAATGAGTCGGGGAATCAACACTTAGCAACCCC
* *
54752261 TCGGGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATATGGTGGAATCAGTACTTAGCAA
1 TCGGGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAA
54752326 CCACCAATGAGTCGGGGAATCAACACTTAGCAACCCC
66 CCACCAATGAGTCGGGGAATCAACACTTAGCAACCCC
54752363 CTTTATATTC
Statistics
Matches: 94, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
102 94 1.00
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.22
Consensus pattern (102 bp):
TCGGGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAA
CCACCAATGAGTCGGGGAATCAACACTTAGCAACCCC
Found at i:54759658 original size:33 final size:33
Alignment explanation
Indices: 54759616--54759837 Score: 116
Period size: 33 Copynumber: 6.4 Consensus size: 33
54759606 GTGGATTCAG
54759616 CACTTAGCAACCACCAATGAGTCGGGGAATCAA
1 CACTTAGCAACCACCAATGAGTCGGGGAATCAA
* * * *
54759649 CACTTAGCAACCCCTTTCACATTTAATATACAGTGGG-ATCAG
1 CACTTAGCAACCAC---CA-A--TGA-GT-C-G-GGGAATCAA
* *
54759691 CACTTAGCAACCACCAATGATTCGGGGAATCAG
1 CACTTAGCAACCACCAATGAGTCGGGGAATCAA
* *
54759724 CACTTAGCAACC-CC--T-CG--GGGGAATCAG
1 CACTTAGCAACCACCAATGAGTCGGGGAATCAA
* * *
54759751 CACTTAGCAAGCCCCTTCACATTTAAGATATGGTGGAATCAA
1 CACTTAGCAA-CCAC--CA-A--TGAG-T-CGG-GGAATCAA
*
54759793 CACTTAGCAACCACCAATGAGTCAGGGAATCAA
1 CACTTAGCAACCACCAATGAGTCGGGGAATCAA
54759826 CACTTAGCAACC
1 CACTTAGCAACC
54759838 CCTTGGGGAA
Statistics
Matches: 148, Mismatches: 15, Indels: 52
0.69 0.07 0.24
Matches are distributed among these distances:
27 20 0.14
28 2 0.01
29 1 0.01
30 1 0.01
31 1 0.01
32 5 0.03
33 51 0.34
34 2 0.01
35 2 0.01
36 8 0.05
37 2 0.01
38 2 0.01
39 6 0.04
40 1 0.01
41 6 0.04
42 35 0.24
43 3 0.02
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.20
Consensus pattern (33 bp):
CACTTAGCAACCACCAATGAGTCGGGGAATCAA
Found at i:54759750 original size:27 final size:28
Alignment explanation
Indices: 54759714--54759766 Score: 99
Period size: 27 Copynumber: 1.9 Consensus size: 28
54759704 CCAATGATTC
54759714 GGGGAATCAGCACTTAGCAA-CCCCTCG
1 GGGGAATCAGCACTTAGCAAGCCCCTCG
54759741 GGGGAATCAGCACTTAGCAAGCCCCT
1 GGGGAATCAGCACTTAGCAAGCCCCT
54759767 TCACATTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 20 0.80
28 5 0.20
ACGTcount: A:0.26, C:0.32, G:0.26, T:0.15
Consensus pattern (28 bp):
GGGGAATCAGCACTTAGCAAGCCCCTCG
Found at i:54759770 original size:102 final size:100
Alignment explanation
Indices: 54759639--54759867 Score: 341
Period size: 102 Copynumber: 2.3 Consensus size: 100
54759629 CCAATGAGTC
* * * *
54759639 GGGGAATCAACACTTAGCAACCCCTTTCACATTTAATATACAGTGGGATCAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCC-TTCACATTTAAGATACAGTGGAATCAACACTTAGCAACCA
* * *
54759704 CCAATGATTCGGGGAATCAGCACTTAGCAACCCCTCG
65 CCAATGAGTCAGGGAATCAACACTTAGCAACCCCT-G
**
54759741 GGGGAATCAGCACTTAGCAAGCCCCTTCACATTTAAGATATGGTGGAATCAACACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAA-CCCCTTCACATTTAAGATACAGTGGAATCAACACTTAGCAACCA
*
54759806 CCAATGAGTCAGGGAATCAACACTTAGCAACCCCTT
65 CCAATGAGTCAGGGAATCAACACTTAGCAACCCCTG
54759842 GGGGAATCAGCACTTAGCAACCCCTT
1 GGGGAATCAGCACTTAGCAACCCCTT
54759868 TATATTCAAT
Statistics
Matches: 116, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
100 6 0.05
101 20 0.17
102 86 0.74
103 4 0.03
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (100 bp):
GGGGAATCAGCACTTAGCAACCCCTTCACATTTAAGATACAGTGGAATCAACACTTAGCAACCAC
CAATGAGTCAGGGAATCAACACTTAGCAACCCCTG
Found at i:54759846 original size:26 final size:26
Alignment explanation
Indices: 54759817--54759867 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
54759807 CAATGAGTCA
54759817 GGGAATCAACACTTAGCAACCCCTTG
1 GGGAATCAACACTTAGCAACCCCTTG
*
54759843 GGGAATCAGCACTTAGCAACCCCTT
1 GGGAATCAACACTTAGCAACCCCTT
54759868 TATATTCAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.20
Consensus pattern (26 bp):
GGGAATCAACACTTAGCAACCCCTTG
Found at i:54766663 original size:85 final size:85
Alignment explanation
Indices: 54766520--54766696 Score: 309
Period size: 85 Copynumber: 2.1 Consensus size: 85
54766510 TAAACACCAA
* * *
54766520 TCTTATGTTGCATGTGGGATAGGTCTTGTATAAATTCAATATTCGATTATCGTGCTTCTTATTGT
1 TCTTATGTTGCATGTGAGATAGGTCTTGTATAAATTCAATATTCGATCATCATGCTTCTTATTGT
54766585 TCAACAGATTCCAAGGGTTG
66 TCAACAGATTCCAAGGGTTG
*
54766605 TCTTATGTTGCATGTGAGATAGGTCTTGTATAAATTCAATATTCGATCGTCATGCTTCTTATTGT
1 TCTTATGTTGCATGTGAGATAGGTCTTGTATAAATTCAATATTCGATCATCATGCTTCTTATTGT
*
54766670 TCAATAGATTCCAAGGGTTG
66 TCAACAGATTCCAAGGGTTG
54766690 TCTTATG
1 TCTTATG
54766697 CACGTTCGTA
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
85 87 1.00
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.42
Consensus pattern (85 bp):
TCTTATGTTGCATGTGAGATAGGTCTTGTATAAATTCAATATTCGATCATCATGCTTCTTATTGT
TCAACAGATTCCAAGGGTTG
Found at i:54769754 original size:49 final size:49
Alignment explanation
Indices: 54769697--54769937 Score: 315
Period size: 49 Copynumber: 4.9 Consensus size: 49
54769687 TCCATATAGA
* *
54769697 ACTACACTTCTTTTATTTTATTTTGATTAGAATAAGGTTTTTCAACCTT
1 ACTACACTTCTTCTATTTTATATTGATTAGAATAAGGTTTTTCAACCTT
* * * **
54769746 ACTACACTTCATCTATTTTATATTGATTAAAATAAGGTGTTGGAACCTT
1 ACTACACTTCTTCTATTTTATATTGATTAGAATAAGGTTTTTCAACCTT
* *
54769795 ACTACAC-TCATTCTATTTTACATTGATTAGAATAAGGTTTTTCAACCCT
1 ACTACACTTC-TTCTATTTTATATTGATTAGAATAAGGTTTTTCAACCTT
* * * **
54769844 ACTACACTTCATCTATTTTATATTGATTAAAATAAGGTGTTGGAACCTT
1 ACTACACTTCTTCTATTTTATATTGATTAGAATAAGGTTTTTCAACCTT
*
54769893 ACTACAC-TCATTCTATTTTACATTGATTAGAATAAGGTTTTTCAA
1 ACTACACTTC-TTCTATTTTATATTGATTAGAATAAGGTTTTTCAA
54769938 ACTATAAATA
Statistics
Matches: 162, Mismatches: 27, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
48 4 0.02
49 156 0.96
50 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.10, T:0.43
Consensus pattern (49 bp):
ACTACACTTCTTCTATTTTATATTGATTAGAATAAGGTTTTTCAACCTT
Found at i:54769821 original size:98 final size:98
Alignment explanation
Indices: 54769697--54769937 Score: 430
Period size: 98 Copynumber: 2.5 Consensus size: 98
54769687 TCCATATAGA
* ** *
54769697 ACTACACTTC-TTTTATTTTATTTTGATTAGAATAAGGTTTTTCAACCTTACTACACTTCATCTA
1 ACTACAC-TCATTCTATTTTACATTGATTAGAATAAGGTTTTTCAACCCTACTACACTTCATCTA
54769761 TTTTATATTGATTAAAATAAGGTGTTGGAACCTT
65 TTTTATATTGATTAAAATAAGGTGTTGGAACCTT
54769795 ACTACACTCATTCTATTTTACATTGATTAGAATAAGGTTTTTCAACCCTACTACACTTCATCTAT
1 ACTACACTCATTCTATTTTACATTGATTAGAATAAGGTTTTTCAACCCTACTACACTTCATCTAT
54769860 TTTATATTGATTAAAATAAGGTGTTGGAACCTT
66 TTTATATTGATTAAAATAAGGTGTTGGAACCTT
54769893 ACTACACTCATTCTATTTTACATTGATTAGAATAAGGTTTTTCAA
1 ACTACACTCATTCTATTTTACATTGATTAGAATAAGGTTTTTCAA
54769938 ACTATAAATA
Statistics
Matches: 138, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
97 2 0.01
98 136 0.99
ACGTcount: A:0.31, C:0.16, G:0.10, T:0.43
Consensus pattern (98 bp):
ACTACACTCATTCTATTTTACATTGATTAGAATAAGGTTTTTCAACCCTACTACACTTCATCTAT
TTTATATTGATTAAAATAAGGTGTTGGAACCTT
Found at i:54774370 original size:49 final size:49
Alignment explanation
Indices: 54774308--54774436 Score: 172
Period size: 49 Copynumber: 2.6 Consensus size: 49
54774298 ACTACACTTT
* *
54774308 TATTTTATTTTGATTAGAATAAGGTTTTTCAACCTTACTACACT-TAATC
1 TATTTGATATTGATTAGAATAAGGTTTTTCAACCTTACTACACTCT-ATC
* * *
54774357 TATTTGATATTGATTAGAATAAGGTGTTTT-AACCTTGCTACACTCTTTT
1 TATTTGATATTGATTAGAATAAGGT-TTTTCAACCTTACTACACTCTATC
*
54774406 TATTTGACATTGATTAGAATAAGGTTTTTCA
1 TATTTGATATTGATTAGAATAAGGTTTTTCA
54774437 TCCTATAAAT
Statistics
Matches: 71, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
48 4 0.06
49 62 0.87
50 5 0.07
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (49 bp):
TATTTGATATTGATTAGAATAAGGTTTTTCAACCTTACTACACTCTATC
Found at i:54775399 original size:17 final size:17
Alignment explanation
Indices: 54775374--54775408 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
54775364 GGTTAACACT
*
54775374 AAAAAAGACTAAATTAC
1 AAAAAAGACAAAATTAC
*
54775391 AAAATAGACAAAATTAC
1 AAAAAAGACAAAATTAC
54775408 A
1 A
54775409 CAATTAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.66, C:0.11, G:0.06, T:0.17
Consensus pattern (17 bp):
AAAAAAGACAAAATTAC
Found at i:54777439 original size:17 final size:18
Alignment explanation
Indices: 54777400--54777440 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
54777390 GGGTTCGCAT
54777400 AAGGGGCTTGCACATGCA
1 AAGGGGCTTGCACATGCA
* *
54777418 AAGGGGTTTGTACATG-A
1 AAGGGGCTTGCACATGCA
54777435 AAGGGG
1 AAGGGG
54777441 GGTTTACATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.29, C:0.12, G:0.39, T:0.20
Consensus pattern (18 bp):
AAGGGGCTTGCACATGCA
Found at i:54779814 original size:27 final size:27
Alignment explanation
Indices: 54779775--54779830 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
54779765 ATAAATTTTT
*
54779775 TAGCATAATTTTTACAAAGGATGCAAA
1 TAGCATAAGTTTTACAAAGGATGCAAA
54779802 TAGCATAAGTTTTACAAAGGATGCAAA
1 TAGCATAAGTTTTACAAAGGATGCAAA
54779829 TA
1 TA
54779831 AATCTCTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.29
Consensus pattern (27 bp):
TAGCATAAGTTTTACAAAGGATGCAAA
Found at i:54780647 original size:6 final size:6
Alignment explanation
Indices: 54780638--54780675 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
54780628 CAGGAGCAGG
54780638 AGCATT AGCATT AGCATT AGCATT AGCATT AGCATT AG
1 AGCATT AGCATT AGCATT AGCATT AGCATT AGCATT AG
54780676 AAGATGGTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (6 bp):
AGCATT
Found at i:54782248 original size:14 final size:14
Alignment explanation
Indices: 54782195--54782261 Score: 53
Period size: 14 Copynumber: 4.5 Consensus size: 14
54782185 ATTTCACTTA
*
54782195 AATTAATTAATGATG
1 AATTAATTAAT-ATT
* *
54782210 GATTAATTATAATAAT
1 AATTAA-T-TAATATT
54782226 AACTTAATTAATATT
1 AA-TTAATTAATATT
**
54782241 AATTAATTAAGGTT
1 AATTAATTAATATT
54782255 AATTAAT
1 AATTAAT
54782262 ATTTAACCAT
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
14 17 0.40
15 13 0.31
16 4 0.10
17 8 0.19
ACGTcount: A:0.48, C:0.01, G:0.07, T:0.43
Consensus pattern (14 bp):
AATTAATTAATATT
Found at i:54782555 original size:22 final size:20
Alignment explanation
Indices: 54782519--54782560 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
54782509 TCATTGTTGA
*
54782519 GAAATTGATGAATTAGGCTT
1 GAAATTGATGAATTAAGCTT
54782539 GAAATTGATAGATATTAAGCTT
1 GAAATTGAT-GA-ATTAAGCTT
54782561 AGATAATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 2 0.11
22 8 0.42
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.36
Consensus pattern (20 bp):
GAAATTGATGAATTAAGCTT
Found at i:54783344 original size:19 final size:19
Alignment explanation
Indices: 54783322--54783364 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
54783312 GTGCAGGTTT
** *
54783322 ATGCAATTTGTGTGTTAGG
1 ATGCAATTCCTGTGCTAGG
*
54783341 ATGCACTTCCTGTGCTAGG
1 ATGCAATTCCTGTGCTAGG
54783360 ATGCA
1 ATGCA
54783365 CTTCGTGCAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.16, G:0.28, T:0.35
Consensus pattern (19 bp):
ATGCAATTCCTGTGCTAGG
Found at i:54783365 original size:19 final size:19
Alignment explanation
Indices: 54783332--54783368 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
54783322 ATGCAATTTG
*
54783332 TGTGTTAGGATGCACTTCC
1 TGTGCTAGGATGCACTTCC
54783351 TGTGCTAGGATGCACTTC
1 TGTGCTAGGATGCACTTC
54783369 GTGCACCAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.22, G:0.27, T:0.35
Consensus pattern (19 bp):
TGTGCTAGGATGCACTTCC
Found at i:54783414 original size:19 final size:19
Alignment explanation
Indices: 54783341--54783427 Score: 86
Period size: 19 Copynumber: 4.6 Consensus size: 19
54783331 GTGTGTTAGG
* * * *
54783341 ATGCACTTCCTGTGCTAGG
1 ATGCACTTCGTGCGCCAGA
*
54783360 ATGCACTTCGTGCACCAGA
1 ATGCACTTCGTGCGCCAGA
54783379 ATGCACTTCGTGCGCCAGA
1 ATGCACTTCGTGCGCCAGA
* *
54783398 ATGCACTACGTGTGCCA-A
1 ATGCACTTCGTGCGCCAGA
*
54783416 GATGCGCTTCGT
1 -ATGCACTTCGT
54783428 TCACCAGTGC
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
18 1 0.02
19 56 0.98
ACGTcount: A:0.21, C:0.29, G:0.25, T:0.25
Consensus pattern (19 bp):
ATGCACTTCGTGCGCCAGA
Found at i:54785445 original size:68 final size:67
Alignment explanation
Indices: 54785351--54785551 Score: 200
Period size: 68 Copynumber: 3.0 Consensus size: 67
54785341 ATTATTTTAA
* * *
54785351 TATTTAAATATTTAATTTAATTTAATACTTATCTTAAAAGTATTTTATTACTTTAATATTAAAGT
1 TATTT-AATATTAAATTTAATTTAATATTTATCTTAAAAGTATTATATTACTTTAATATTAAAGT
54785416 GAT
65 GAT
* * * *
54785419 TATCTTAATATTAAATTTAATTTAATATTTATCTT-GAAG-ATAAACATT-CTATT-AT-TTTAA
1 TAT-TTAATATTAAATTTAATTTAATATTTATCTTAAAAGTAT-TATATTACT-TTAATATTAAA
*
54785479 -T-AA
63 GTGAT
* * * *
54785482 GATTTAATATTAAATTTAATCTAATATTTATCTTAATAAATATTATATTAATTTAATATTAAAGT
1 TATTTAATATTAAATTTAATTTAATATTTATCTTAA-AAGTATTATATTACTTTAATATTAAAGT
54785547 GAT
65 GAT
54785550 TA
1 TA
54785552 AGTTTAATCA
Statistics
Matches: 104, Mismatches: 18, Indels: 22
0.72 0.12 0.15
Matches are distributed among these distances:
62 30 0.29
63 3 0.03
64 9 0.09
65 9 0.09
66 10 0.10
67 9 0.09
68 32 0.31
69 2 0.02
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (67 bp):
TATTTAATATTAAATTTAATTTAATATTTATCTTAAAAGTATTATATTACTTTAATATTAAAGTG
AT
Found at i:54785492 original size:62 final size:59
Alignment explanation
Indices: 54785423--54785539 Score: 171
Period size: 62 Copynumber: 1.9 Consensus size: 59
54785413 AGTGATTATC
* * *
54785423 TTAATATTAAATTTAATTTAATATTTATCTTGAAGATAAACATTCTATTATTTTAATAAGAT
1 TTAATATTAAATTTAATCTAATATTTATCTT--A-ATAAACATTATATTAATTTAATAAGAT
*
54785485 TTAATATTAAATTTAATCTAATATTTATCTTAATAAATATTATATTAATTTAATA
1 TTAATATTAAATTTAATCTAATATTTATCTTAATAAACATTATATTAATTTAATA
54785540 TTAAAGTGAT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 20 0.39
60 1 0.02
62 30 0.59
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.50
Consensus pattern (59 bp):
TTAATATTAAATTTAATCTAATATTTATCTTAATAAACATTATATTAATTTAATAAGAT
Found at i:54788914 original size:25 final size:25
Alignment explanation
Indices: 54788854--54788914 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 25
54788844 CTCCTAAATT
*
54788854 TTAATTTAATTATCTAATTTTTCAA
1 TTAATTAAATTATCTAATTTTTCAA
* *
54788879 TTTATTGAATTAT-TAATATTTT-ATA
1 TTAATTAAATTATCTAAT-TTTTCA-A
54788904 TTAATTAAATT
1 TTAATTAAATT
54788915 TTTTATAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
24 5 0.17
25 25 0.83
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (25 bp):
TTAATTAAATTATCTAATTTTTCAA
Found at i:54795636 original size:17 final size:17
Alignment explanation
Indices: 54795614--54795657 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
54795604 ATTAATGGGT
*
54795614 TTACATAATCTCCTAGA
1 TTACATAATCTCCCAGA
*
54795631 TTACATAATCTCCCGGA
1 TTACATAATCTCCCAGA
*
54795648 TTACAAAATC
1 TTACATAATC
54795658 AAATATTATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.32
Consensus pattern (17 bp):
TTACATAATCTCCCAGA
Found at i:54797121 original size:21 final size:21
Alignment explanation
Indices: 54797097--54797136 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
54797087 ACTTGTAATG
* *
54797097 ATTTTTTTTTCAATTTTCTAT
1 ATTTTTTTTTAAAATTTCTAT
54797118 ATTTTTTTTTAAAATTTCT
1 ATTTTTTTTTAAAATTTCT
54797137 TGAACTTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (21 bp):
ATTTTTTTTTAAAATTTCTAT
Found at i:54797187 original size:20 final size:20
Alignment explanation
Indices: 54797163--54797205 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
54797153 TTTTAAAAAT
*
54797163 ATTTTAAACA-TTTTTCATA
1 ATTTTTAACACTTTTTCATA
*
54797182 ATTTTTACCACTTTTTCATA
1 ATTTTTAACACTTTTTCATA
54797202 ATTT
1 ATTT
54797206 ATATAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.30, C:0.14, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTTTTAACACTTTTTCATA
Found at i:54797286 original size:17 final size:16
Alignment explanation
Indices: 54797264--54797307 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
54797254 ATGCAATTTC
54797264 TTTATATTTTATATATT
1 TTTATATTTTATATA-T
* *
54797281 TTTATAATTTTCTGTAT
1 TTTAT-ATTTTATATAT
54797298 TTTATATTTT
1 TTTATATTTT
54797308 TGTACTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 5 0.21
17 11 0.46
18 8 0.33
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.70
Consensus pattern (16 bp):
TTTATATTTTATATAT
Found at i:54797316 original size:15 final size:17
Alignment explanation
Indices: 54797281--54797317 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
54797271 TTTATATATT
*
54797281 TTTATAATTTTCTGTAT
1 TTTATAATTTTCTGTAC
54797298 TTTAT-ATTTT-TGTAC
1 TTTATAATTTTCTGTAC
54797313 TTTAT
1 TTTAT
54797318 TGTTTTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 9 0.47
16 5 0.26
17 5 0.26
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68
Consensus pattern (17 bp):
TTTATAATTTTCTGTAC
Found at i:54797370 original size:21 final size:20
Alignment explanation
Indices: 54797344--54797387 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
54797334 AAATTAATAA
*
54797344 TTTTATTATTTTTATGACTTT
1 TTTTATAATTTTTATGA-TTT
54797365 TTTTATAATTTTTATGATTT
1 TTTTATAATTTTTATGATTT
54797385 TTT
1 TTT
54797388 AAAAAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.73
Consensus pattern (20 bp):
TTTTATAATTTTTATGATTT
Found at i:54797395 original size:21 final size:21
Alignment explanation
Indices: 54797351--54797398 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
54797341 TAATTTTATT
* *
54797351 ATTTTTATGACTTTTTTTATA
1 ATTTTTATGACTTTTTTAAAA
54797372 ATTTTTATGA-TTTTTTAAAA
1 ATTTTTATGACTTTTTTAAAA
*
54797392 AATTTTA
1 ATTTTTA
54797399 AATATAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.62
Consensus pattern (21 bp):
ATTTTTATGACTTTTTTAAAA
Found at i:54798201 original size:37 final size:40
Alignment explanation
Indices: 54798141--54798242 Score: 138
Period size: 38 Copynumber: 2.6 Consensus size: 40
54798131 GGCCCATTTT
*
54798141 TTTAATAAATACAAAAAATTTATTTT-AAAATATTTTAAAA
1 TTTAAAAAATA-AAAAAATTTATTTTAAAAATATTTTAAAA
54798181 -TTAAAAAATAAAAAAA-TTATTTTAAAAATATTTTAAAA
1 TTTAAAAAATAAAAAAATTTATTTTAAAAATATTTTAAAA
* *
54798219 TTTTAAAAAATAAATATATTTATT
1 -TTTAAAAAATAAAAAAATTTATT
54798243 ATATCAGACC
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
37 7 0.13
38 20 0.36
39 9 0.16
40 14 0.25
41 5 0.09
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (40 bp):
TTTAAAAAATAAAAAAATTTATTTTAAAAATATTTTAAAA
Found at i:54801130 original size:27 final size:26
Alignment explanation
Indices: 54801092--54801146 Score: 60
Period size: 27 Copynumber: 2.1 Consensus size: 26
54801082 TAAAAATACA
*
54801092 AATTTTAGAATT-TTTAT-AAATATTTG
1 AATTTTAAAATTATTT-TCAAAT-TTTG
54801118 AATTTTAAAAATTATTTTCAAATTTTG
1 AATTTT-AAAATTATTTTCAAATTTTG
54801145 AA
1 AA
54801147 AATTTCTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
26 6 0.24
27 12 0.48
28 7 0.28
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (26 bp):
AATTTTAAAATTATTTTCAAATTTTG
Found at i:54806700 original size:15 final size:16
Alignment explanation
Indices: 54806661--54806707 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
54806651 CACTTTTTTA
*
54806661 ATCATCC-CTGATCTC
1 ATCATCCTCTCATCTC
54806676 ATCATCCCTCTCATCTC
1 ATCAT-CCTCTCATCTC
54806693 -TCATCCTCTC-TCTC
1 ATCATCCTCTCATCTC
54806707 A
1 A
54806708 AATATCTTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
14 4 0.14
15 11 0.39
16 6 0.21
17 7 0.25
ACGTcount: A:0.17, C:0.45, G:0.02, T:0.36
Consensus pattern (16 bp):
ATCATCCTCTCATCTC
Found at i:54812712 original size:50 final size:50
Alignment explanation
Indices: 54812570--54812866 Score: 265
Period size: 50 Copynumber: 5.8 Consensus size: 50
54812560 GATAATAACA
* ** * * *
54812570 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTTATGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGG
* * * * * ** *
54812619 TACCAATGTCATATCCCAAATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
** * * **
54812669 TGCCCGTGCCATGTCCTAGACATTGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* ** *
54812719 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTGTCTCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
54812769 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATTTCAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--GG
* * *
54812824 ATGCCAATGCCATGTCCCAGATATTGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
54812867 TTACCCAAAT
Statistics
Matches: 197, Mismatches: 43, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
48 1 0.01
49 36 0.18
50 117 0.59
53 3 0.02
55 1 0.01
56 39 0.20
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:54816399 original size:20 final size:20
Alignment explanation
Indices: 54816364--54816421 Score: 91
Period size: 20 Copynumber: 2.9 Consensus size: 20
54816354 GTTTTTCTAG
54816364 TTTAAATTATTT-TGTTAAAT
1 TTTAAATT-TTTATGTTAAAT
*
54816384 TTTAACTTTTTATGTTAAAT
1 TTTAAATTTTTATGTTAAAT
54816404 TTTAAATTTTTATGTTAA
1 TTTAAATTTTTATGTTAA
54816422 TAAAGTGGGT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 3 0.09
20 32 0.91
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (20 bp):
TTTAAATTTTTATGTTAAAT
Found at i:54822694 original size:15 final size:15
Alignment explanation
Indices: 54822674--54822702 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
54822664 GTGCGTAACA
54822674 CATATCCTTCAAGAT
1 CATATCCTTCAAGAT
54822689 CATATCCTTCAAGA
1 CATATCCTTCAAGA
54822703 ATCAATAAAA
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:0.34, C:0.28, G:0.07, T:0.31
Consensus pattern (15 bp):
CATATCCTTCAAGAT
Found at i:54827610 original size:21 final size:21
Alignment explanation
Indices: 54827571--54827611 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
54827561 TAGAAACAGG
* **
54827571 AATGATCTTAATGGTAATCCA
1 AATGATCGTAATGAAAATCCA
54827592 AATGATCGTAATGAAAATCC
1 AATGATCGTAATGAAAATCC
54827612 TCTCATTAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (21 bp):
AATGATCGTAATGAAAATCCA
Found at i:54830646 original size:93 final size:93
Alignment explanation
Indices: 54830481--54830669 Score: 299
Period size: 93 Copynumber: 2.0 Consensus size: 93
54830471 GGTAAGGCAT
* * * * *
54830481 TTTATTTCTTCCTAGATGCTTATTTAGGATATAATCAAATTTCTATAGCACTTGAAGATCAAGAG
1 TTTATTGCTTCCTAGATGCTTATTCAAGATATAATCAAATTTCCATAGCACTTAAAGATCAAGAG
54830546 AGAACAACTTTCACGTGTCCATATGGTA
66 AGAACAACTTTCACGTGTCCATATGGTA
* *
54830574 TTTATTGCTTCCTAGATGGTTATTCAAGATATAATCAAATTTCCATAGCACTTAAATATCAAGAG
1 TTTATTGCTTCCTAGATGCTTATTCAAGATATAATCAAATTTCCATAGCACTTAAAGATCAAGAG
54830639 A-AGACAACTTTCACGTGTCCATATGGTA
66 AGA-ACAACTTTCACGTGTCCATATGGTA
54830667 TTT
1 TTT
54830670 TTATATTTAG
Statistics
Matches: 88, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
92 1 0.01
93 87 0.99
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (93 bp):
TTTATTGCTTCCTAGATGCTTATTCAAGATATAATCAAATTTCCATAGCACTTAAAGATCAAGAG
AGAACAACTTTCACGTGTCCATATGGTA
Found at i:54835532 original size:15 final size:15
Alignment explanation
Indices: 54835509--54835538 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
54835499 TGGTTTCCAT
54835509 TAAAAAAAGGAAAAA
1 TAAAAAAAGGAAAAA
*
54835524 TAAAGAAAGGAAAAA
1 TAAAAAAAGGAAAAA
54835539 GGAGAATAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.07
Consensus pattern (15 bp):
TAAAAAAAGGAAAAA
Found at i:54835557 original size:21 final size:19
Alignment explanation
Indices: 54835533--54835572 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
54835523 ATAAAGAAAG
54835533 GAAAAAGGAGAATAAATATAT
1 GAAAAA-GAGAAT-AATATAT
*
54835554 GAAAAAGTGAATAATATAT
1 GAAAAAGAGAATAATATAT
54835573 TTTTCATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 5 0.28
21 6 0.33
ACGTcount: A:0.60, C:0.00, G:0.17, T:0.23
Consensus pattern (19 bp):
GAAAAAGAGAATAATATAT
Found at i:54837599 original size:2 final size:2
Alignment explanation
Indices: 54837592--54837617 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
54837582 TTCTTAGGAT
54837592 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
54837618 GTCCTGAATT
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:54842079 original size:16 final size:16
Alignment explanation
Indices: 54842042--54842083 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
54842032 TTAATCATAT
*
54842042 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
54842058 TT-AAATATATTATAA
1 TTAAAATATATTATAA
54842073 TTAAAATATAT
1 TTAAAATATAT
54842084 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:54842090 original size:14 final size:15
Alignment explanation
Indices: 54842051--54842092 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
54842041 TTTAAACATA
*
54842051 ATTATTATTAAATAT
1 ATTATAATTAAATAT
54842066 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
54842080 A-TATAATTTAATA
1 ATTATAATTAAATA
54842093 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:54842163 original size:107 final size:107
Alignment explanation
Indices: 54842040--54842362 Score: 601
Period size: 107 Copynumber: 3.0 Consensus size: 107
54842030 ATTTAATCAT
54842040 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
54842105 ATTAATATTCTTATATGAATTTACTCAAATCATAATATAGATA
65 ATTAATATTCTTATATGAATTTACTCAAATCATAATATAGATA
*
54842148 ATTTAACATAATTATTATAAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
54842213 TTAATATTCTTATATGAATTTACTCAAATCATAATATAGATA
66 TTAATATTCTTATATGAATTTACTCAAATCATAATATAGATA
54842255 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
* *
54842320 TCAATATTCTTATATGAATTTACTAAAATCATAATATATGATA
66 TTAATATTCTTATATGAATTTACTCAAATCATAATATA-GATA
54842363 CTATAAAATA
Statistics
Matches: 210, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
107 202 0.96
108 8 0.04
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (107 bp):
ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
TTAATATTCTTATATGAATTTACTCAAATCATAATATAGATA
Found at i:54842295 original size:16 final size:16
Alignment explanation
Indices: 54842252--54842297 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
54842242 CATAATATAG
*
54842252 ATAATTTAACATA-ATT
1 ATAA-TTAAAATATATT
*
54842268 ATTATT-AAATATATT
1 ATAATTAAAATATATT
54842283 ATAATTAAAATATAT
1 ATAATTAAAATATAT
54842298 AATTTAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 4 0.16
15 10 0.40
16 11 0.44
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
ATAATTAAAATATATT
Found at i:54842304 original size:14 final size:15
Alignment explanation
Indices: 54842252--54842306 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
54842242 CATAATATAG
54842252 ATAATTTAACATA-ATT
1 ATAA-TTAA-ATATATT
*
54842268 ATTATTAAATATATT
1 ATAATTAAATATATT
54842283 ATAATTAAA-ATA-T
1 ATAATTAAATATATT
*
54842296 ATAATTTAATA
1 ATAATTAAATA
54842307 AAATTCTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 9 0.26
14 7 0.21
15 15 0.44
16 3 0.09
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAATTAAATATATT
Found at i:54842482 original size:47 final size:44
Alignment explanation
Indices: 54842413--54842680 Score: 167
Period size: 47 Copynumber: 5.9 Consensus size: 44
54842403 TTAATTAAAA
*
54842413 TATATG-ATTTAATAAAATTTAAAATAATTATACCTAATAAATTTTCT
1 TATATGAATTT-ATATAATTTAAAATAATTAT---TAATAAATTTTCT
* * *
54842460 TATATGAATTTGTATAATTTAAAATAATTATTATTAAATATAAT-T
1 TATATGAATTTATATAATTTAAAATAATTATTAATAAAT-T-TTCT
* * *
54842505 TA-AT-AATAATATATAATTTCATAA-AATTCTTGATAATAAATTTTCT
1 TATATGAAT-TTATATAATTT-AAAATAATT-AT--TAATAAATTTTCT
* * *
54842551 TATATGAATTTATATAATTTAAAATAATTAATATTAAATATAAT-T
1 TATATGAATTTATATAATTTAAAATAATTATTAATAAAT-T-TTCT
* ** *
54842596 TA-AT-AATGATATATAATTTCTTAAAATTCTTGA-TAATAAATTTTTT
1 TATATGAAT-TTATATAA--T-TTAAAATAATT-ATTAATAAATTTTCT
* *
54842642 TATATGAATTTATATAATTTAAAATAATTAATATTAAAT
1 TATATGAATTTATATAATTTAAAATAATTATTAATAAAT
54842681 ATAATTTAAT
Statistics
Matches: 173, Mismatches: 25, Indels: 49
0.70 0.10 0.20
Matches are distributed among these distances:
43 7 0.04
44 54 0.31
45 15 0.09
46 14 0.08
47 72 0.42
48 11 0.06
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (44 bp):
TATATGAATTTATATAATTTAAAATAATTATTAATAAATTTTCT
Found at i:54842485 original size:101 final size:95
Alignment explanation
Indices: 54842370--54842706 Score: 376
Period size: 91 Copynumber: 3.5 Consensus size: 95
54842360 ATACTATAAA
* *
54842370 ATATAATTTGAAATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTTAA
1 ATATAATTTAAAATAATTAATATTAAATATAATTTAA-TAAAATATAT-ATTTAATAAAATTTAA
* *
54842435 AATAATTATACCTAATAAATTTTCTTATATGAATTT
64 AAT-CTT-GA--TAATAAATTTTCTTATATGAATTT
* * *
54842471 GTATAATTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTCATAAAA--T--
1 ATATAATTTAAAATAATTAATATTAAATATAATTTAATAA-AATATAT-ATTTAATAAAATTTAA
54842532 --TCTTGATAATAAATTTTCTTATATGAATTT
64 AATCTTGATAATAAATTTTCTTATATGAATTT
*
54842562 ATATAATTTAAAATAATTAATATTAAATATAATTTAAT--AATGATATA--TAAT---TTCTTAA
1 ATATAATTTAAAATAATTAATATTAAATATAATTTAATAAAAT-ATATATTTAATAAAAT-TTAA
*
54842620 AATTCTTGATAATAAATTTTTTTATATGAATTT
64 AA-TCTTGATAATAAATTTTCTTATATGAATTT
*
54842653 ATATAATTTAAAATAATTAATATTAAATATAATTTAATAATGATATATAATTTA
1 ATATAATTTAAAATAATTAATATTAAATATAATTTAATAA-AATATAT-ATTTA
54842707 TACATTTAAC
Statistics
Matches: 206, Mismatches: 14, Indels: 37
0.80 0.05 0.14
Matches are distributed among these distances:
86 4 0.02
88 4 0.02
89 4 0.02
91 127 0.62
93 5 0.02
94 5 0.02
95 1 0.00
96 2 0.01
99 1 0.00
100 3 0.01
101 50 0.24
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (95 bp):
ATATAATTTAAAATAATTAATATTAAATATAATTTAATAAAATATATATTTAATAAAATTTAAAA
TCTTGATAATAAATTTTCTTATATGAATTT
Found at i:54842522 original size:44 final size:43
Alignment explanation
Indices: 54842472--54842706 Score: 197
Period size: 44 Copynumber: 5.2 Consensus size: 43
54842462 TATGAATTTG
*
54842472 TATAATTTAAAATAATTATTATTAAATATAATTTAATAATAATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
** * * * *
54842516 TATAATTTCATAAAATTCTTGATAATAAAT-T-TTCTTATATGAATTTA
1 TATAA-TT--TAAAATAATTAATATTAAATATAAT-TTA-AT-AATATA
54842563 TATAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
** * * ** *
54842607 TATAATTTCTTAAAATTCTTGATAATAAAT-TTTTTTATATGAATTTA
1 TATAA--T-TTAAAATAATTAATATTAAATATAATTTA-AT-AATATA
54842654 TATAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
54842698 TATAATTTA
1 TATAATTTA
54842707 TACATTTAAC
Statistics
Matches: 148, Mismatches: 27, Indels: 32
0.71 0.13 0.15
Matches are distributed among these distances:
43 6 0.04
44 60 0.41
45 13 0.09
46 13 0.09
47 50 0.34
48 6 0.04
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (43 bp):
TATAATTTAAAATAATTAATATTAAATATAATTTAATAATATA
Found at i:54842543 original size:91 final size:91
Alignment explanation
Indices: 54842447--54842705 Score: 473
Period size: 91 Copynumber: 2.8 Consensus size: 91
54842437 TAATTATACC
* *
54842447 TAATAAATTTTCTTATATGAATTTGTATAATTTAAAATAATTATTATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
54842512 AATATATAATTTCATAAAATTCTTGA
66 GATATATAATTTCATAAAATTCTTGA
54842538 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
54842603 GATATATAATTTCTTAAAATTCTTGA
66 GATATATAATTTCATAAAATTCTTGA
*
54842629 TAATAAATTTTTTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
54842694 GATATATAATTT
66 GATATATAATTT
54842706 ATACATTTAA
Statistics
Matches: 163, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
91 163 1.00
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (91 bp):
TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
GATATATAATTTCATAAAATTCTTGA
Found at i:54842553 original size:221 final size:226
Alignment explanation
Indices: 54842145--54842562 Score: 561
Period size: 221 Copynumber: 1.9 Consensus size: 226
54842135 CATAATATAG
*
54842145 ATAATTTAACATAATTATTATAAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAA
1 ATAATTTAACATAATTAATATAAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAA
* * * *
54842210 TAATTAATATTCTTATATGAATTTACTCAAATCATAATATAGATAATTTAACATAATTATTATTA
66 TAATTAATATACCTATATAAATTTA-TCAAATCATAATATAGATAATTTAAAATAATTATTATTA
*
54842275 AATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATT
130 AATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATAAATATTCTTATATGAATT
54842340 TACTAAAATCATAATATATGATACTATAAAAT
195 TACTAAAATCATAATATATGATACTATAAAAT
* * *
54842372 ATAATTTGAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAA-T-TTA
1 ATAATTT-AACATAATTAATATAAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTA
** *
54842434 A-AA-TAATTATACCTA-ATAAATTT-TCTTAT-ATGAAT-TTGTATAATTTAAAATAATTATTA
65 ATAATTAA-TATACCTATATAAATTTATCAAATCAT-AATATAG-ATAATTTAAAATAATTATTA
* * *
54842493 TTAAATATAATT-TAA-TAATAATATATAATTTCATAAAATTCTTGATAATAAATTTTCTTATAT
127 TTAAATAT-ATTATAATTAA-AATATATAATTTAATAAAATTCTTAATAATAAATATTCTTATAT
54842556 GAATTTA
190 GAATTTA
54842563 TATAATTTAA
Statistics
Matches: 170, Mismatches: 15, Indels: 18
0.84 0.07 0.09
Matches are distributed among these distances:
220 7 0.04
221 84 0.49
222 3 0.02
223 10 0.06
224 8 0.05
225 4 0.02
226 1 0.01
227 51 0.30
228 2 0.01
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (226 bp):
ATAATTTAACATAATTAATATAAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAA
TAATTAATATACCTATATAAATTTATCAAATCATAATATAGATAATTTAAAATAATTATTATTAA
ATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATAAATATTCTTATATGAATTT
ACTAAAATCATAATATATGATACTATAAAAT
Found at i:54843724 original size:17 final size:17
Alignment explanation
Indices: 54843702--54843737 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
54843692 GCACCTAATA
54843702 TAACTCATATTTCAAAT
1 TAACTCATATTTCAAAT
54843719 TAACTCATATTTCAAAT
1 TAACTCATATTTCAAAT
54843736 TA
1 TA
54843738 CAGCAAAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.42
Consensus pattern (17 bp):
TAACTCATATTTCAAAT
Found at i:54846304 original size:20 final size:21
Alignment explanation
Indices: 54846279--54846322 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 21
54846269 TTAATTTCAG
54846279 TTTACA-TTATCGTGG-TTTTA
1 TTTACAGTT-TCGTGGTTTTTA
54846299 TTTACAGTTTCGTGGTTTTTA
1 TTTACAGTTTCGTGGTTTTTA
54846320 TTT
1 TTT
54846323 TATCTACTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.16, C:0.09, G:0.16, T:0.59
Consensus pattern (21 bp):
TTTACAGTTTCGTGGTTTTTA
Found at i:54849772 original size:41 final size:41
Alignment explanation
Indices: 54849707--54849793 Score: 129
Period size: 41 Copynumber: 2.1 Consensus size: 41
54849697 TAACTTATTT
*
54849707 TATTTTTTAAAAAGAAAAAATATATATATATGAATTCCCTA
1 TATTTTTTAAAAAGAAAAAATATATATATACGAATTCCCTA
* * * *
54849748 TATTTTTTAAAAAGCAAAAGTATATATATACGATTTTCCTA
1 TATTTTTTAAAAAGAAAAAATATATATATACGAATTCCCTA
54849789 TATTT
1 TATTT
54849794 GATAATAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.43
Consensus pattern (41 bp):
TATTTTTTAAAAAGAAAAAATATATATATACGAATTCCCTA
Found at i:54849916 original size:27 final size:27
Alignment explanation
Indices: 54849885--54849940 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
54849875 AAATCGATCT
* *
54849885 AAATTGTAGTGGTTATTCAGCAAATTA
1 AAATTCTAATGGTTATTCAGCAAATTA
54849912 AAATTCTAATGGTTATTCAGCAAATTA
1 AAATTCTAATGGTTATTCAGCAAATTA
54849939 AA
1 AA
54849941 TTTTATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (27 bp):
AAATTCTAATGGTTATTCAGCAAATTA
Found at i:54851225 original size:30 final size:30
Alignment explanation
Indices: 54851189--54851245 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
54851179 ATATATTATG
54851189 TATCATTATATTAAATTACCTAAATATCAT
1 TATCATTATATTAAATTACCTAAATATCAT
**
54851219 TATCATTATATTAAATTATTTAAATAT
1 TATCATTATATTAAATTACCTAAATAT
54851246 AATTTATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (30 bp):
TATCATTATATTAAATTACCTAAATATCAT
Found at i:54852427 original size:3 final size:3
Alignment explanation
Indices: 54852419--54852472 Score: 58
Period size: 3 Copynumber: 18.7 Consensus size: 3
54852409 TAATTTTTAT
* * * *
54852419 TTA TTA TTA TTA TTA TTA TTA TGA TTT TTA TTA -TC TTG TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
54852465 TTA TTA TT
1 TTA TTA TT
54852473 TTTTAAAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
2 3 0.07
3 39 0.93
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:54852448 original size:31 final size:31
Alignment explanation
Indices: 54852411--54852471 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
54852401 TTAAGCTTTA
54852411 ATTTTTATT-TATTATTATTATTATTATTATG
1 ATTTTTATTATATTATTATT-TTATTATTATG
* *
54852442 ATTTTTATTATCTTGTTATTTTATTATTAT
1 ATTTTTATTATATTATTATTTTATTATTAT
54852472 TTTTTAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 19 0.70
32 8 0.30
ACGTcount: A:0.26, C:0.02, G:0.03, T:0.69
Consensus pattern (31 bp):
ATTTTTATTATATTATTATTTTATTATTATG
Found at i:54862471 original size:45 final size:45
Alignment explanation
Indices: 54862422--54862560 Score: 149
Period size: 45 Copynumber: 3.1 Consensus size: 45
54862412 AGCACCACAC
* * * *
54862422 TTATAGTCAATAGTACTCTGTGAAATCAGTACATAGCAACCACCT
1 TTATAATCAATGGTACTCGGTGAAATCAGTACATAGCAATCACCT
* *
54862467 TTATACTCAATGGTAC-CGGGTGAATTCAGTACATAGCAATCA-CT
1 TTATAATCAATGGTACTC-GGTGAAATCAGTACATAGCAATCACCT
* * *
54862511 TATATAACCATTGGTA-TCCGGTGAAATCTGTACATAGCAATCACCT
1 T-TATAATCAATGGTACT-CGGTGAAATCAGTACATAGCAATCACCT
54862557 TTAT
1 TTAT
54862561 TTTCATTAAT
Statistics
Matches: 79, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
44 4 0.05
45 71 0.90
46 4 0.05
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (45 bp):
TTATAATCAATGGTACTCGGTGAAATCAGTACATAGCAATCACCT
Found at i:54864182 original size:18 final size:18
Alignment explanation
Indices: 54864159--54864212 Score: 83
Period size: 18 Copynumber: 3.1 Consensus size: 18
54864149 CCTGTCCATG
54864159 GGCCGGGCGGCCCGGCCC
1 GGCCGGGCGGCCCGGCCC
54864177 GGCCGGGCGGCCCGGCCC
1 GGCCGGGCGGCCCGGCCC
* *
54864195 GGCCCGACGGCCC-GCCC
1 GGCCGGGCGGCCCGGCCC
54864212 G
1 G
54864213 AAATATGGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
17 5 0.15
18 29 0.85
ACGTcount: A:0.02, C:0.52, G:0.46, T:0.00
Consensus pattern (18 bp):
GGCCGGGCGGCCCGGCCC
Found at i:54864417 original size:22 final size:22
Alignment explanation
Indices: 54864392--54864444 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
54864382 TTTAAAATAC
*
54864392 TTTAAAAATATTTTTTTTTATT
1 TTTAAAAATATTTTTTTGTATT
*
54864414 TTT-AAAATATTTTTTTGTGTT
1 TTTAAAAATATTTTTTTGTATT
54864435 TATTAAAAAT
1 T-TTAAAAAT
54864445 CGGGCCGGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 17 0.63
22 5 0.19
23 5 0.19
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (22 bp):
TTTAAAAATATTTTTTTGTATT
Found at i:54873589 original size:5 final size:5
Alignment explanation
Indices: 54873579--54873616 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
54873569 TTTTTATATA
54873579 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATT
54873617 TTATATTGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
ATTAT
Found at i:54881800 original size:44 final size:44
Alignment explanation
Indices: 54881733--54881911 Score: 286
Period size: 44 Copynumber: 4.1 Consensus size: 44
54881723 GTAGATAAAA
* *
54881733 TAATATTAAAATAACCTACACTAATTAGAGTTTAAATGGGAAAC
1 TAATATTAAAATAACCTACACTAATCAAAGTTTAAATGGGAAAC
* * *
54881777 TAATATTAAAATAATCTATACTAATCAGAGTTTAAATGGGAAAC
1 TAATATTAAAATAACCTACACTAATCAAAGTTTAAATGGGAAAC
*
54881821 TAATATTAAAATAACCTACACTAATCAAAGTTTAAATAGGAAAC
1 TAATATTAAAATAACCTACACTAATCAAAGTTTAAATGGGAAAC
* *
54881865 TAATATTAAAATAACCTACACTAATCAAAGTTTAAGTGAGAAAC
1 TAATATTAAAATAACCTACACTAATCAAAGTTTAAATGGGAAAC
54881909 TAA
1 TAA
54881912 AAACAGAGTT
Statistics
Matches: 125, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 125 1.00
ACGTcount: A:0.50, C:0.12, G:0.09, T:0.29
Consensus pattern (44 bp):
TAATATTAAAATAACCTACACTAATCAAAGTTTAAATGGGAAAC
Found at i:54881845 original size:21 final size:21
Alignment explanation
Indices: 54881819--54881889 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 21
54881809 TAAATGGGAA
54881819 ACTAATATTAAAATAACCTAC
1 ACTAATATTAAAATAACCTAC
* ** *
54881840 ACTAATCAAAGTTTAAAT-A-GGAA
1 ACTAAT---A-TTAAAATAACCTAC
54881863 ACTAATATTAAAATAACCTAC
1 ACTAATATTAAAATAACCTAC
54881884 ACTAAT
1 ACTAAT
54881890 CAAAGTTTAA
Statistics
Matches: 36, Mismatches: 8, Indels: 12
0.64 0.14 0.21
Matches are distributed among these distances:
19 6 0.17
20 2 0.06
21 13 0.36
23 7 0.19
24 2 0.06
25 6 0.17
ACGTcount: A:0.52, C:0.15, G:0.04, T:0.28
Consensus pattern (21 bp):
ACTAATATTAAAATAACCTAC
Found at i:54892642 original size:459 final size:459
Alignment explanation
Indices: 54891784--54892705 Score: 1727
Period size: 459 Copynumber: 2.0 Consensus size: 459
54891774 TGAAATCATA
54891784 AAAACTTATGGTGAATGCTCTTTGCCCAATTTGTAGCTCATTTGTTTCGGGAATGCGCCTTCACA
1 AAAACTTATGGTGAATGCTCTTTGCCCAATTTGTAGCTCATTTGTTTCGGGAATGCGCCTTCACA
54891849 AAGTTGGTCTGGCAGGAAATAGGAGTGGCTCCCTCGACCACAAACAAGGGCTAAGATTGGAGATA
66 AAGTTGGTCTGGCAGGAAATAGGAGTGGCTCCCTCGACCACAAACAAGGGCTAAGATTGGAGATA
* *
54891914 GTGGTTAGCATTAGAAATTGGTTGCTGAGAGCAACGAGGAAGATTTAGTTGGTCCTAATTTGGTC
131 GTGGTTAGCATTAGAAATTGGTTGCTGAGAGCAACGAGAAAGATTTAGTTGGTCCTAATTTGGCC
*
54891979 AATGATAAGGATGATGATTTCTTGTTGGTTTCAGCAAGTGAAAGCTTCAGGTTTACGTCCGAGTG
196 AATGATAAGGAAGATGATTTCTTGTTGGTTTCAGCAAGTGAAAGCTTCAGGTTTACGTCCGAGTG
* *
54892044 GATCTTAGATTCGATGTTTTCTTTCCACATGTGTCCCAAGAGGGACTAGTTCTCCACATACAGTT
261 GATCCTAGATTCGAGGTTTTCTTTCCACATGTGTCCCAAGAGGGACTAGTTCTCCACATACAGTT
54892109 TAGTTGAATGTGAAGTTGTGCACACGGGGAATGGTTCACCCAATAAGGTAATCGATACTGGTACT
326 TAGTTGAATGTGAAGTTGTGCACACGGGGAATGGTTCACCCAATAAGGTAATCGATACTGGTACT
54892174 GTTTAGATCAGGATGCACAATGGGACAATTAGGACACTGCCAAATGTCAGGCACGTGCCTGACGT
391 GTTTAGATCAGGATGCACAATGGGACAATTAGGACACTGCCAAATGTCAGGCACGTGCCTGACGT
54892239 AAAG
456 AAAG
*
54892243 AAAACTTATGGTGAATGCTCTTTGCCCAATTTGTAGCTCATTTGTTTCGGGAATGCGCCTTTACA
1 AAAACTTATGGTGAATGCTCTTTGCCCAATTTGTAGCTCATTTGTTTCGGGAATGCGCCTTCACA
* *
54892308 AAGTTGGTCTGGCAGGAAATAGGAGTGGCTCCCTCGGCCACAAACAGGGGCTAAGATTGGAGATA
66 AAGTTGGTCTGGCAGGAAATAGGAGTGGCTCCCTCGACCACAAACAAGGGCTAAGATTGGAGATA
* *
54892373 GTGGTTAGCATTAGAAATTGGTTGTTGAGAGCAACGAGAAAGATTTAGTTGGTGCTAATTTGGCC
131 GTGGTTAGCATTAGAAATTGGTTGCTGAGAGCAACGAGAAAGATTTAGTTGGTCCTAATTTGGCC
54892438 AATGATAAGGAAGATGATTTCTTGTTGGTTTCAGCAAGTGAAAGCTTCAGGTTTACGTCCGAGTG
196 AATGATAAGGAAGATGATTTCTTGTTGGTTTCAGCAAGTGAAAGCTTCAGGTTTACGTCCGAGTG
* *
54892503 GATCCTAGATTTGAGGTTTTCTTTCCACATGTGTCCCAAGAGGGACTGGTTCTCCACATACAGTT
261 GATCCTAGATTCGAGGTTTTCTTTCCACATGTGTCCCAAGAGGGACTAGTTCTCCACATACAGTT
54892568 TAGTTGAATGTGAAGTTGTGCACACGGGGAATGGTTCACCCAATAAGGTAATCGATACTGGTACT
326 TAGTTGAATGTGAAGTTGTGCACACGGGGAATGGTTCACCCAATAAGGTAATCGATACTGGTACT
*
54892633 GTTTAGATCAGGATGCACAATGGGACAATTAGGACACTGTCAAATGTCAGGCACGTGCCTGACGT
391 GTTTAGATCAGGATGCACAATGGGACAATTAGGACACTGCCAAATGTCAGGCACGTGCCTGACGT
54892698 AAAG
456 AAAG
54892702 AAAA
1 AAAA
54892706 ATCTAATCTC
Statistics
Matches: 450, Mismatches: 13, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
459 450 1.00
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (459 bp):
AAAACTTATGGTGAATGCTCTTTGCCCAATTTGTAGCTCATTTGTTTCGGGAATGCGCCTTCACA
AAGTTGGTCTGGCAGGAAATAGGAGTGGCTCCCTCGACCACAAACAAGGGCTAAGATTGGAGATA
GTGGTTAGCATTAGAAATTGGTTGCTGAGAGCAACGAGAAAGATTTAGTTGGTCCTAATTTGGCC
AATGATAAGGAAGATGATTTCTTGTTGGTTTCAGCAAGTGAAAGCTTCAGGTTTACGTCCGAGTG
GATCCTAGATTCGAGGTTTTCTTTCCACATGTGTCCCAAGAGGGACTAGTTCTCCACATACAGTT
TAGTTGAATGTGAAGTTGTGCACACGGGGAATGGTTCACCCAATAAGGTAATCGATACTGGTACT
GTTTAGATCAGGATGCACAATGGGACAATTAGGACACTGCCAAATGTCAGGCACGTGCCTGACGT
AAAG
Found at i:54893891 original size:44 final size:45
Alignment explanation
Indices: 54893814--54893901 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 45
54893804 ATAATTGTAA
* ** *
54893814 ATTAAATTATAGTTATTTTTAAATGTGCGATTATCA-AAATTTTT
1 ATTAAATTATAATTATTTTTAAATGAACAATTATCACAAATTTTT
* *
54893858 ATTAAATTATAATTATTTTTGAATGAATAATTATCACAAATTTT
1 ATTAAATTATAATTATTTTTAAATGAACAATTATCACAAATTTT
54893902 AATTTACGTC
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
44 30 0.81
45 7 0.19
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.49
Consensus pattern (45 bp):
ATTAAATTATAATTATTTTTAAATGAACAATTATCACAAATTTTT
Found at i:54894374 original size:14 final size:14
Alignment explanation
Indices: 54894328--54894376 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
54894318 AAAAAATATA
54894328 TATTTA-TATTATAT
1 TATTTACTATT-TAT
*
54894342 TATATTACTATTTAC
1 TAT-TTACTATTTAT
*
54894357 TATTTACTATTTTT
1 TATTTACTATTTAT
54894371 TATTTA
1 TATTTA
54894377 TTAAATTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 18 0.60
15 8 0.27
16 4 0.13
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (14 bp):
TATTTACTATTTAT
Found at i:54897411 original size:59 final size:60
Alignment explanation
Indices: 54897258--54897426 Score: 232
Period size: 59 Copynumber: 2.8 Consensus size: 60
54897248 AGCACCGAAT
* * * *
54897258 TTTTTAACGAATAACTGTAAATTAAATTATAATTATAATCATCACACTTTATCATCAAAA
1 TTTTTAACTAATAACTGTAAATTAAATTATAATTATAATTATCACAATTTATCAGCAAAA
* * * *
54897318 CTTTTAACTAATAACTGTAAATTAAATTATAATTATAGTTATCACAATTTA-GAGCCAAA
1 TTTTTAACTAATAACTGTAAATTAAATTATAATTATAATTATCACAATTTATCAGCAAAA
* * *
54897377 TTTTTAACTAATAATTGTGAATTAAATTATAATTATAATTATCTCAATTT
1 TTTTTAACTAATAACTGTAAATTAAATTATAATTATAATTATCACAATTT
54897427 TTCCTATATT
Statistics
Matches: 96, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
59 50 0.52
60 46 0.48
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (60 bp):
TTTTTAACTAATAACTGTAAATTAAATTATAATTATAATTATCACAATTTATCAGCAAAA
Found at i:54897614 original size:6 final size:6
Alignment explanation
Indices: 54897591--54897629 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
54897581 TATTTAAATA
*
54897591 ATAATT ATAAGTG A-AATT ATAATT ATAATT ATAATT ATA
1 ATAATT ATAA-TT ATAATT ATAATT ATAATT ATAATT ATA
54897630 TGATCACAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 2 0.07
6 25 0.86
7 2 0.07
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (6 bp):
ATAATT
Done.