Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 169 of 198
Found at i:53114054 original size:43 final size:40
Alignment explanation
Indices: 53113964--53114058 Score: 102
Period size: 43 Copynumber: 2.2 Consensus size: 40
53113954 AAGTCAATTA
* *
53113964 TGTAAGTTATGTACGTGTATAAGTTATGTAAGTTATGTAT
1 TGTAAGTTATGTAAGTGTATAAGTAATGTAAGTTATGTAT
*
53114004 TAAGTAAGTTATGTAAGT-TATCAAAGTAATGTATGTTATGTAAGT
1 T--GTAAGTTATGTAAGTGTAT--AAGTAATGTAAGTTATGT-A-T
53114049 TGTAAGTTAT
1 TGTAAGTTAT
53114059 TATGTATTAT
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
40 1 0.02
41 3 0.07
42 14 0.30
43 25 0.54
44 1 0.02
45 2 0.04
ACGTcount: A:0.34, C:0.02, G:0.21, T:0.43
Consensus pattern (40 bp):
TGTAAGTTATGTAAGTGTATAAGTAATGTAAGTTATGTAT
Found at i:53114075 original size:26 final size:26
Alignment explanation
Indices: 53114039--53114288 Score: 317
Period size: 26 Copynumber: 9.3 Consensus size: 26
53114029 GTAATGTATG
53114039 TTATGTAAGTTGTAAGTTATTATGTA
1 TTATGTAAGTTGTAAGTTATTATGTA
*
53114065 TTATGTAAGTTGTAAGTTA-AATGTA
1 TTATGTAAGTTGTAAGTTATTATGTA
53114090 TTATGTAAGTTGTAAGTTATTATGTA
1 TTATGTAAGTTGTAAGTTATTATGTA
*
53114116 TTATGTAAGTTGTAAGTTA-AATGTA
1 TTATGTAAGTTGTAAGTTATTATGTA
*
53114141 TTATGTAAGTTGTAGGTTATTATGTA
1 TTATGTAAGTTGTAAGTTATTATGTA
*
53114167 TTATGTAAGTTATTTAAGTTACCTAAGTTAAATGTA
1 TTATGTAAG-T-TGTAAG-T---T-A-TT--ATGTA
*
53114203 TTATGTAAGTTGTAAGTTATAATGTA
1 TTATGTAAGTTGTAAGTTATTATGTA
53114229 TTATGTAAGTTGTAAGTTATTATGTA
1 TTATGTAAGTTGTAAGTTATTATGTA
*
53114255 TTATGTAAGTTATGTAAGTTA-AATGTA
1 TTATGTAAG-T-TGTAAGTTATTATGTA
53114282 TTATGTA
1 TTATGTA
53114289 GGTTATGTAA
Statistics
Matches: 199, Mismatches: 11, Indels: 27
0.84 0.05 0.11
Matches are distributed among these distances:
25 47 0.24
26 96 0.48
27 14 0.07
28 14 0.07
29 2 0.01
30 1 0.01
32 1 0.01
33 2 0.01
34 7 0.04
35 1 0.01
36 14 0.07
ACGTcount: A:0.33, C:0.01, G:0.19, T:0.47
Consensus pattern (26 bp):
TTATGTAAGTTGTAAGTTATTATGTA
Found at i:53114107 original size:51 final size:51
Alignment explanation
Indices: 53114039--53114288 Score: 331
Period size: 51 Copynumber: 4.6 Consensus size: 51
53114029 GTAATGTATG
53114039 TTATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTAAATGTA
1 TTATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTAAATGTA
53114090 TTATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTAAATGTA
1 TTATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTAAATGTA
*
53114141 TTATGTAAGTTGTAGGTTATTATGTATTATGTAAGTTATTTAAGTTACCTAAGTTAAATGTA
1 TTATGTAAGTTGTAAGTTATTATGTATTATGTAAG----TT--G-----TAAGTTAAATGTA
* *
53114203 TTATGTAAGTTGTAAGTTATAATGTATTATGTAAGTTGTAAGTTATTATGTA
1 TTATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTA-AATGTA
*
53114255 TTATGTAAGTTATGTAAGTTA-AATGTATTATGTA
1 TTATGTAAG-T-TGTAAGTTATTATGTATTATGTA
53114289 GGTTATGTAA
Statistics
Matches: 181, Mismatches: 4, Indels: 26
0.86 0.02 0.12
Matches are distributed among these distances:
51 92 0.51
52 14 0.08
53 14 0.08
54 9 0.05
55 2 0.01
56 1 0.01
57 1 0.01
58 2 0.01
62 46 0.25
ACGTcount: A:0.33, C:0.01, G:0.19, T:0.47
Consensus pattern (51 bp):
TTATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTAAATGTA
Found at i:53114235 original size:19 final size:19
Alignment explanation
Indices: 53114213--53114294 Score: 70
Period size: 19 Copynumber: 4.5 Consensus size: 19
53114203 TTATGTAAGT
53114213 TGTAAGTTATAATGTATTA
1 TGTAAGTTATAATGTATTA
*
53114232 TGTAAGTTGTAA-GTTATTA
1 TGTAAGTTATAATG-TATTA
53114251 TGT-A--T-T-ATGTAAGTTA
1 TGTAAGTTATAATGT-A-TTA
53114267 TGTAAGTTA-AATGTATTA
1 TGTAAGTTATAATGTATTA
*
53114285 TGTAGGTTAT
1 TGTAAGTTAT
53114295 GTAAGTTGTG
Statistics
Matches: 51, Mismatches: 2, Indels: 20
0.70 0.03 0.27
Matches are distributed among these distances:
14 2 0.04
15 3 0.06
16 7 0.14
17 1 0.02
18 13 0.25
19 21 0.41
20 4 0.08
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.48
Consensus pattern (19 bp):
TGTAAGTTATAATGTATTA
Found at i:53114251 original size:88 final size:88
Alignment explanation
Indices: 53113996--53114275 Score: 349
Period size: 88 Copynumber: 3.3 Consensus size: 88
53113986 GTTATGTAAG
* * *
53113996 TTATGTATTAAGTAAGTTATGTAAGTTATCAAAG---TAATGTATGTTATGTAAGTTGTAAGTTA
1 TTATGTATTATGTAAGTTATGTAAGTTACCTAAGTTATAATGTA--TTATGTAAGTTGTAAGTTA
*
53114058 TTATGTATTATGTAAGTTGTAAGTTA
64 -AATGTATTATGTAAGTTGTAAGTTA
*
53114084 -AATGTATTATGTAAG-T-TGTAAG-T---T-A--T-T-ATGTATTATGTAAGTTGTAAGTTAAA
1 TTATGTATTATGTAAGTTATGTAAGTTACCTAAGTTATAATGTATTATGTAAGTTGTAAGTTAAA
*
53114137 TGTATTATGTAAGTTGTAGGTTA
66 TGTATTATGTAAGTTGTAAGTTA
*
53114160 TTATGTATTATGTAAGTTATTTAAGTTACCTAAGTTA-AATGTATTATGTAAGTTGTAAGTTATA
1 TTATGTATTATGTAAGTTATGTAAGTTACCTAAGTTATAATGTATTATGTAAGTTGTAAGTTA-A
53114224 ATGTATTATGTAAGTTGTAAGTTA
65 ATGTATTATGTAAGTTGTAAGTTA
53114248 TTATGTATTATGTAAGTTATGTAAGTTA
1 TTATGTATTATGTAAGTTATGTAAGTTA
53114276 AATGTATTAT
Statistics
Matches: 169, Mismatches: 9, Indels: 28
0.82 0.04 0.14
Matches are distributed among these distances:
76 23 0.14
77 33 0.20
78 1 0.01
79 10 0.06
80 3 0.02
83 1 0.01
84 2 0.01
85 6 0.04
86 2 0.01
87 37 0.22
88 51 0.30
ACGTcount: A:0.34, C:0.01, G:0.19, T:0.46
Consensus pattern (88 bp):
TTATGTATTATGTAAGTTATGTAAGTTACCTAAGTTATAATGTATTATGTAAGTTGTAAGTTAAA
TGTATTATGTAAGTTGTAAGTTA
Found at i:53114295 original size:88 final size:84
Alignment explanation
Indices: 53114090--53114303 Score: 295
Period size: 88 Copynumber: 2.4 Consensus size: 84
53114080 GTTAAATGTA
*
53114090 TTATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTA
1 TTATGTAAGTT-AAAG-TATTATGTATTATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTA
*
53114155 GGTTATTATGTATTATGTAAG
64 AGTTATTATGTATTATGTAAG
* *
53114176 TTATTTAAGTTACCTAAGT-TAAATGTATTATGTAAGTTGTAAGTTATAATGTATTATGTAAGTT
1 TTATGTAAGTTA---AAGTAT-TATGTATTATGTAAGTTGTAAGTTA-AATGTATTATGTAAGTT
53114240 GTAAGTTATTATGTATTATGTAAG
61 GTAAGTTATTATGTATTATGTAAG
53114264 TTATGTAAGTTAAATGTATTATGTAGGTTATGTAAGTTGT
1 TTATGTAAGTTAAA-GTATTATGTA--TTATGTAAGTTGT
53114304 GTAAGAGATT
Statistics
Matches: 113, Mismatches: 6, Indels: 16
0.84 0.04 0.12
Matches are distributed among these distances:
85 2 0.02
86 18 0.16
87 26 0.23
88 67 0.59
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.47
Consensus pattern (84 bp):
TTATGTAAGTTAAAGTATTATGTATTATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAG
TTATTATGTATTATGTAAG
Found at i:53114338 original size:43 final size:43
Alignment explanation
Indices: 53114291--53114376 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
53114281 ATTATGTAGG
* *
53114291 TTATGTAAGTTGTGTAAGAGATTTAAGTTATGTGAGTTTTGTA
1 TTATGTAAGTTATGTAAGAGATTTAAGTTATGTAAGTTTTGTA
** *
53114334 TTATGTAAGTTATGTAAGTTATTTAGGTTATGTAAGTTTTGTA
1 TTATGTAAGTTATGTAAGAGATTTAAGTTATGTAAGTTTTGTA
53114377 ATGTACAAGT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.28, C:0.00, G:0.23, T:0.49
Consensus pattern (43 bp):
TTATGTAAGTTATGTAAGAGATTTAAGTTATGTAAGTTTTGTA
Found at i:53114869 original size:18 final size:19
Alignment explanation
Indices: 53114843--53114880 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
53114833 TGTGTTCAGA
53114843 TGAAAATTTTT-AAATTTT
1 TGAAAATTTTTAAAATTTT
*
53114861 TGAAGATTTTTAAAATTTT
1 TGAAAATTTTTAAAATTTT
53114880 T
1 T
53114881 AAACTCTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (19 bp):
TGAAAATTTTTAAAATTTT
Found at i:53114878 original size:9 final size:9
Alignment explanation
Indices: 53114845--53114883 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
53114835 TGTTCAGATG
53114845 AAAATTTTT
1 AAAATTTTT
53114854 -AAATTTTT
1 AAAATTTTT
*
53114862 GAAGATTTTT
1 -AAAATTTTT
53114872 AAAATTTTT
1 AAAATTTTT
53114881 AAA
1 AAA
53114884 CTCTACAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
8 8 0.31
9 11 0.42
10 7 0.27
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (9 bp):
AAAATTTTT
Found at i:53115548 original size:31 final size:32
Alignment explanation
Indices: 53115482--53115563 Score: 114
Period size: 31 Copynumber: 2.6 Consensus size: 32
53115472 GAACTATTTC
* *
53115482 CCAT-TTAGCAGCAGAAATCAATAGAAGCGGTA
1 CCATCTTAGCAGCAAAAACCAATAGAA-CGGTA
53115514 CCATCTTAGCAGCAAAAACCAATAGAA-GGTA
1 CCATCTTAGCAGCAAAAACCAATAGAACGGTA
*
53115545 CCATCTTAGCTGCAAAAAC
1 CCATCTTAGCAGCAAAAAC
53115564 TAATTAAAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
31 22 0.48
32 4 0.09
33 20 0.43
ACGTcount: A:0.41, C:0.23, G:0.17, T:0.18
Consensus pattern (32 bp):
CCATCTTAGCAGCAAAAACCAATAGAACGGTA
Found at i:53116317 original size:22 final size:20
Alignment explanation
Indices: 53116263--53116302 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
53116253 AAAGGATGAA
53116263 GAAAGGATGAGGGGAAATCG
1 GAAAGGATGAGGGGAAATCG
53116283 GAAAGGATGAGGGGAAATCG
1 GAAAGGATGAGGGGAAATCG
53116303 CAGAAAGACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.45, T:0.10
Consensus pattern (20 bp):
GAAAGGATGAGGGGAAATCG
Found at i:53119898 original size:43 final size:43
Alignment explanation
Indices: 53119851--53120049 Score: 233
Period size: 43 Copynumber: 4.6 Consensus size: 43
53119841 TCTCTAAACA
* ** *
53119851 CGCCGCTAAAAGTCTTGTTCTTTAGCGGCATTTTCGGGGAAAG
1 CGCCGCTAAAAGTCTTGTTCTTTAGCGGCGTTTTTAGGAAAAG
* *
53119894 CGCCGCTAAAGGTCTTGTTCTTTAGCGACGTTTTTATGG-AAAG
1 CGCCGCTAAAAGTCTTGTTCTTTAGCGGCGTTTTTA-GGAAAAG
* *
53119937 CGCCG-TTAAAGTTCTTGTTCTTTAGCGGCGTTTTTATGAAAAG
1 CGCCGCTAAAAG-TCTTGTTCTTTAGCGGCGTTTTTAGGAAAAG
* *
53119980 CGCCG-TTAAAGTTCTTGTTCTTTAGCGGCGTTTTTGGGAAAAG
1 CGCCGCTAAAAG-TCTTGTTCTTTAGCGGCGTTTTTAGGAAAAG
* * *
53120023 CGCCGCTAAAGGTCATGATCTTTAGCG
1 CGCCGCTAAAAGTCTTGTTCTTTAGCG
53120050 ACGCTTATTT
Statistics
Matches: 137, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
42 5 0.04
43 126 0.92
44 6 0.04
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (43 bp):
CGCCGCTAAAAGTCTTGTTCTTTAGCGGCGTTTTTAGGAAAAG
Found at i:53134147 original size:48 final size:48
Alignment explanation
Indices: 53134091--53134187 Score: 158
Period size: 48 Copynumber: 2.0 Consensus size: 48
53134081 CTTGTATATG
*
53134091 AGTTATGTCTATACTTGATCATAACTTTTTATAAATAAATACATTATA
1 AGTTATGTCCATACTTGATCATAACTTTTTATAAATAAATACATTATA
* * *
53134139 AGTTATGTCCATATTTGGTCATAACTTTTTATAAATAAATATATTATA
1 AGTTATGTCCATACTTGATCATAACTTTTTATAAATAAATACATTATA
53134187 A
1 A
53134188 CACTTTTATA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.44
Consensus pattern (48 bp):
AGTTATGTCCATACTTGATCATAACTTTTTATAAATAAATACATTATA
Found at i:53136560 original size:25 final size:25
Alignment explanation
Indices: 53136496--53136552 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
53136486 CAGCTCGAGA
53136496 GAGCTTACCGATATTTAGCTCATCT
1 GAGCTTACCGATATTTAGCTCATCT
53136521 GAGCTTACCGATATTTAGCTCATCT
1 GAGCTTACCGATATTTAGCTCATCT
53136546 GAGCTTA
1 GAGCTTA
53136553 TGGTTATTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.35
Consensus pattern (25 bp):
GAGCTTACCGATATTTAGCTCATCT
Found at i:53136567 original size:25 final size:25
Alignment explanation
Indices: 53136496--53136567 Score: 81
Period size: 25 Copynumber: 2.9 Consensus size: 25
53136486 CAGCTCGAGA
* *
53136496 GAGCTTACCGATATTTAGCTCATCT
1 GAGCTTACCGATATTCAACTCATCT
* *
53136521 GAGCTTACCGATATTTAGCTCATCT
1 GAGCTTACCGATATTCAACTCATCT
** *
53136546 GAGCTTATGGTTATTCAACTCA
1 GAGCTTACCGATATTCAACTCA
53136568 GAGGAGCTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (25 bp):
GAGCTTACCGATATTCAACTCATCT
Found at i:53136603 original size:24 final size:25
Alignment explanation
Indices: 53136571--53136627 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
53136561 CAACTCAGAG
* * *
53136571 GAGCTTACCG-TTTACAGCTCGTAA
1 GAGCATACCGATTCACAGCTCATAA
* *
53136595 GAGCATACCGATTCAGAGCTCATAT
1 GAGCATACCGATTCACAGCTCATAA
53136620 GAGCATAC
1 GAGCATAC
53136628 ATGTACAGGA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 9 0.33
25 18 0.67
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (25 bp):
GAGCATACCGATTCACAGCTCATAA
Found at i:53139396 original size:26 final size:28
Alignment explanation
Indices: 53139344--53139398 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
53139334 TTTTTATTAT
* * *
53139344 TATTTATTATTTCTCTCATTTTAGTTCA
1 TATTGATTACTTCTCTCATTGTAGTTCA
53139372 TATTGATTACTTCTCT-ATTGT-GTTCA
1 TATTGATTACTTCTCTCATTGTAGTTCA
53139398 T
1 T
53139399 TTTGTGGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 6 0.25
27 4 0.17
28 14 0.58
ACGTcount: A:0.20, C:0.15, G:0.07, T:0.58
Consensus pattern (28 bp):
TATTGATTACTTCTCTCATTGTAGTTCA
Found at i:53146799 original size:57 final size:58
Alignment explanation
Indices: 53146703--53146822 Score: 172
Period size: 57 Copynumber: 2.1 Consensus size: 58
53146693 AGAAATGGTA
* **
53146703 AAAATGGAGAAATGAGAAATATTTGGAAATGGTTATGGTTTTCTCCAAAATAAAAATG
1 AAAATAGAGAAATGAGAAATATTTGGAAATGAATATGGTTTTCTCCAAAATAAAAATG
* *
53146761 AAAATAGAGAAATG-G-AATCATTTGGAAATGAATGTGGTTTTCTCCAAAATGAAAATG
1 AAAATAGAGAAATGAGAAAT-ATTTGGAAATGAATATGGTTTTCTCCAAAATAAAAATG
53146818 AAAAT
1 AAAAT
53146823 GACCTGAAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
56 3 0.05
57 40 0.71
58 13 0.23
ACGTcount: A:0.46, C:0.06, G:0.20, T:0.28
Consensus pattern (58 bp):
AAAATAGAGAAATGAGAAATATTTGGAAATGAATATGGTTTTCTCCAAAATAAAAATG
Found at i:53147604 original size:45 final size:45
Alignment explanation
Indices: 53147471--53147604 Score: 112
Period size: 45 Copynumber: 3.0 Consensus size: 45
53147461 CTATGTCAAG
*
53147471 GATTGCCAAAACACAATTTCTATCGATTTCTATTAAGGTTCATAT
1 GATTGCCAAAACACAATTTCTATCGATTTATATTAAGGTTCATAT
*** * * * ** *
53147516 GATTGCCAAAGGTCCA--TCAATC-ATACTTAAACAAAGAGGTCATAT
1 GATTGCCAAAACACAATTTCTATCGAT--TTATATTAAG-GTTCATAT
* *
53147561 GATTGCCAAAACACAATTTCTGTCGATTTTTATTAAGGTTCATA
1 GATTGCCAAAACACAATTTCTATCGATTTATATTAAGGTTCATA
53147605 ATAGGTATAC
Statistics
Matches: 62, Mismatches: 21, Indels: 12
0.65 0.22 0.13
Matches are distributed among these distances:
42 2 0.03
43 5 0.08
44 6 0.10
45 37 0.60
46 6 0.10
47 4 0.06
48 2 0.03
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (45 bp):
GATTGCCAAAACACAATTTCTATCGATTTATATTAAGGTTCATAT
Found at i:53149396 original size:23 final size:23
Alignment explanation
Indices: 53149366--53149410 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
53149356 CCCAAATCAT
53149366 GGCAACTGATACCATGTTAAGAA
1 GGCAACTGATACCATGTTAAGAA
53149389 GGCAACTGATACCATGTTAAGA
1 GGCAACTGATACCATGTTAAGA
53149411 GAAAGGGAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (23 bp):
GGCAACTGATACCATGTTAAGAA
Found at i:53151708 original size:40 final size:41
Alignment explanation
Indices: 53151677--53151789 Score: 106
Period size: 44 Copynumber: 2.7 Consensus size: 41
53151667 AACATTTTAA
* *
53151677 AAATTAAAATATAGAAAAATA-ATAATATTAAAAATATAAG
1 AAATTAAAAAATAGAAAAAAATATAATATTAAAAATATAAG
* *
53151717 ACATTAAAAAATAGAAAAAAATATAATATTTCCAAAAATA-AAA
1 AAATTAAAAAATAGAAAAAAATATAATA-TT--AAAAATATAAG
* *
53151760 AAATCACTAAAATA-AAAAAAATCATAATAT
1 AAATTA-AAAAATAGAAAAAAAT-ATAATAT
53151790 GCAAATAATA
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
40 18 0.30
41 6 0.10
42 2 0.03
43 15 0.25
44 19 0.32
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.25
Consensus pattern (41 bp):
AAATTAAAAAATAGAAAAAAATATAATATTAAAAATATAAG
Found at i:53151710 original size:16 final size:15
Alignment explanation
Indices: 53151673--53151729 Score: 53
Period size: 16 Copynumber: 3.7 Consensus size: 15
53151663 TTTAAACATT
*
53151673 TTAAAAATTAAAATA
1 TTAAAAAATAAAATA
53151688 -TAGAAAAATAATAATA
1 TTA-AAAAATAA-AATA
* *
53151704 TTAAAAATATAAGACA
1 TTAAAAA-ATAAAATA
53151720 TTAAAAAATA
1 TTAAAAAATA
53151730 GAAAAAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
14 2 0.06
15 10 0.29
16 17 0.49
17 6 0.17
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.28
Consensus pattern (15 bp):
TTAAAAAATAAAATA
Found at i:53152110 original size:19 final size:21
Alignment explanation
Indices: 53152083--53152121 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
53152073 ATATTTATTT
53152083 AATTATTAAAAATT-ATTTTA
1 AATTATTAAAAATTAATTTTA
*
53152103 AATT-TTAAATATTAATTTT
1 AATTATTAAAAATTAATTTT
53152122 TAAAACTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
AATTATTAAAAATTAATTTTA
Found at i:53153092 original size:2 final size:2
Alignment explanation
Indices: 53153087--53153115 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
53153077 CAAGAACTCA
53153087 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
53153116 CAAGAATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53160824 original size:54 final size:54
Alignment explanation
Indices: 53160755--53160875 Score: 154
Period size: 54 Copynumber: 2.2 Consensus size: 54
53160745 GTGTTTCAAG
** *
53160755 TCAGTGAGTTACATGGCCTAACACATGGCCTGA-CACACGGGAGTGTGTGGTAAC
1 TCAGTGAGTTACATGGCCTAACACACAG-CTGAGCACACGGGAGCGTGTGGTAAC
* * * * *
53160809 TCAGAGAGTTACATGGCCTAGCACACAGCTTAGCATACGGGTGCGTGTGGTAAC
1 TCAGTGAGTTACATGGCCTAACACACAGCTGAGCACACGGGAGCGTGTGGTAAC
53160863 TCAGTGAGTTACA
1 TCAGTGAGTTACA
53160876 CAGGTGTGGG
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
53 3 0.05
54 54 0.95
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.23
Consensus pattern (54 bp):
TCAGTGAGTTACATGGCCTAACACACAGCTGAGCACACGGGAGCGTGTGGTAAC
Found at i:53170664 original size:3 final size:3
Alignment explanation
Indices: 53170658--53170703 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
53170648 TTTTTTTTTA
*
53170658 TAT TAT TAAT T-T TAT TA- TAT TAAT TAT TAT TGT TAT TAT TAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT
53170703 T
1 T
53170704 TCAATACATA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
2 4 0.11
3 27 0.73
4 6 0.16
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:53175754 original size:6 final size:6
Alignment explanation
Indices: 53175743--53175788 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
53175733 GATGATGGAA
*
53175743 AAAAAG AAAAAG AAAAA- AATAAA- AAAAAG AAAGAAG AAAAGG AAAA
1 AAAAAG AAAAAG AAAAAG AA-AAAG AAAAAG AAA-AAG AAAAAG AAAA
53175789 GGAGAGGCCA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
5 5 0.14
6 25 0.69
7 6 0.17
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:53175788 original size:21 final size:22
Alignment explanation
Indices: 53175739--53175788 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
53175729 AAATGATGAT
53175739 GGAAAAAAAGAAAAAGAAAAAAA
1 GGAAAAAAAG-AAAAGAAAAAAA
** *
53175762 TAAAAAAAAG-AAAGAAGAAAA
1 GGAAAAAAAGAAAAGAAAAAAA
53175783 GGAAAA
1 GGAAAA
53175789 GGAGAGGCCA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
21 14 0.64
23 8 0.36
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (22 bp):
GGAAAAAAAGAAAAGAAAAAAA
Found at i:53177486 original size:100 final size:101
Alignment explanation
Indices: 53177309--53177515 Score: 269
Period size: 100 Copynumber: 2.1 Consensus size: 101
53177299 CAGTGAAACG
* *
53177309 GATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCGGTGTAGGGAAACAAATTGAAGTCACGAC
1 GATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCGATGCAGGGAAACAAATTGAAGTCACGAC
* * *
53177374 GGCGAGTTTTGTTTTCCCGACATTGCAATTAAA-AA
66 GGCGAGTATTGTTTCCCCGACAGTGCAATTAAACAA
* ** * *
53177409 GATTGAAGCTATAACGGCT-AATCTTAGC-TCTTTGGCGATGCAGTGAAACAGATTGAAGTCACG
1 GATTGAAGCTACAACGG-TGAATCTTA-CTTCCCTGGCGATGCAGGGAAACAAATTGAAGTCACG
*
53177472 ACGGCGAGTATTGTTTCCCCGACAGTGCAGTTAAACAA
64 ACGGCGAGTATTGTTTCCCCGACAGTGCAATTAAACAA
53177510 -ATTGAA
1 GATTGAA
53177516 AAAAATAATC
Statistics
Matches: 93, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
100 89 0.96
101 4 0.04
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (101 bp):
GATTGAAGCTACAACGGTGAATCTTACTTCCCTGGCGATGCAGGGAAACAAATTGAAGTCACGAC
GGCGAGTATTGTTTCCCCGACAGTGCAATTAAACAA
Found at i:53177656 original size:44 final size:41
Alignment explanation
Indices: 53177517--53178180 Score: 233
Period size: 44 Copynumber: 15.9 Consensus size: 41
53177507 CAAATTGAAA
* * *
53177517 AAAATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGAT-T
1 AAAATAATCCTATCTCCCTGAAGTTGCAGCGGAGCAGATAG
* * * * * *
53177557 AAAATCAGATCTTATCTCTCTAAAGTTGCAG-AGAACAGATTG
1 AAAAT-A-ATCCTATCTCCCTGAAGTTGCAGCGGAGCAGATAG
* *** * *
53177599 CATCCAGTCCTATCTCCCTGAAGTTACAGCGGAGCAGACATAAG
1 AAAATAATCCTATCTCCCTGAAGTTGCAGCGGAGCAG--AT-AG
* *
53177643 AAAATAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGAT-T
1 AAAATAATCCTATCTCCCTGAAGTTGCAGCGGAGCAGATAG
* * * *
53177683 AAAATCAGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGATCG
1 AAAAT-A-ATCCTATCTCCCTGAAGTTGCAGCGGAGCAGATAG
* *** * * * ** *
53177725 CATCCAGTCCTATCTCTCTAAAGTTATAGCGGAGCAAATAGAAG
1 AAAATAATCCTATCTCCCTGAAGTTGCAGCGGAGCAGAT---AG
* * *
53177769 AAAATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGAT-T
1 AAAATAATCCTATCTCCCTGAAGTTGCAGCGGAGCAGATAG
** * * * * * *
53177809 AAAATCAGATATTATCTCTCTAAATTTACAG-AGAGCAGATCG
1 AAAAT-A-ATCCTATCTCCCTGAAGTTGCAGCGGAGCAGATAG
* *** * * *
53177851 CATCCAGTCTTATCTCCCTAAAGTTGCAGCAGAGCAGACAGA-AG
1 AAAATAATCCTATCTCCCTGAAGTTGCAGC-G-G-AG-CAGATAG
* * *
53177895 AAAATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGAT-T
1 AAAATAATCCTATCTCCCTGAAGTTGCAGCGGAGCAGATAG
* ** * *
53177935 AAAATAGATCTTATCTTTCTGAAGTTGCAG-AGAGCAGATCG
1 AAAATA-ATCCTATCTCCCTGAAGTTGCAGCGGAGCAGATAG
* *** *
53177976 CATCCAGTCCTATCTCCCTGAAGTTGCAGCAGAGCAGACAGA-AG
1 AAAATAATCCTATCTCCCTGAAGTTGCAGC-G-G-AG-CAGATAG
* * * * * *
53178020 AAAATAATCATATCTCTCTAAAGTTTCAGTGGAG-TGAATTA-
1 AAAATAATCCTATCTCCCTGAAGTTGCAGCGGAGCAG-A-TAG
* * * ** *
53178061 AAAATAGATCTTATCTCTCTAAAGTTGCA-AAGAACAGAT--
1 AAAATA-ATCCTATCTCCCTGAAGTTGCAGCGGAGCAGATAG
* * * * * *
53178100 CACATCCAGTCCTATCTCCCTAAAGTTGCAGCGGAGCAGGCTGAA
1 AAAAT--AATCCTATCTCCCTGAAGTTGCAGCGGAGCA-GAT-AG
*
53178145 AAAATCAATCCTATCTCCCTGAAGTTGCAGTGGAGC
1 AAAAT-AATCCTATCTCCCTGAAGTTGCAGCGGAGC
53178181 GATTAAAACC
Statistics
Matches: 449, Mismatches: 133, Indels: 80
0.68 0.20 0.12
Matches are distributed among these distances:
39 4 0.01
40 125 0.28
41 79 0.18
42 89 0.20
43 6 0.01
44 135 0.30
45 11 0.02
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (41 bp):
AAAATAATCCTATCTCCCTGAAGTTGCAGCGGAGCAGATAG
Found at i:53177749 original size:126 final size:126
Alignment explanation
Indices: 53177517--53178233 Score: 1046
Period size: 126 Copynumber: 5.7 Consensus size: 126
53177507 CAAATTGAAA
53177517 AAAATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTAAAG
1 AAAATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTAAAG
* * * * *
53177582 TTGCAGAGAACAGATTGCATCCAGTCCTATCTCCCTGAAGTTACAGCGGAGCAGACATAAG
66 TTGCAGAGAGCAGATCGCATCCAGTCCTATCTCCCTAAAGTTGCAGCGGAGCAGACAGAAG
* *
53177643 AAAATAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCAGATCTTATCTCTCTGAAG
1 AAAATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTAAAG
* ** * *
53177708 TTGCAGAGAGCAGATCGCATCCAGTCCTATCTCTCTAAAGTTATAGCGGAGCAAATAGAAG
66 TTGCAGAGAGCAGATCGCATCCAGTCCTATCTCCCTAAAGTTGCAGCGGAGCAGACAGAAG
* *
53177769 AAAATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATATTATCTCTCTAAAT
1 AAAATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTAAAG
* * *
53177834 TTACAGAGAGCAGATCGCATCCAGTCTTATCTCCCTAAAGTTGCAGCAGAGCAGACAGAAG
66 TTGCAGAGAGCAGATCGCATCCAGTCCTATCTCCCTAAAGTTGCAGCGGAGCAGACAGAAG
* *
53177895 AAAATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAAT-AGATCTTATCTTTCTGAAG
1 AAAATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTAAAG
* *
53177959 TTGCAGAGAGCAGATCGCATCCAGTCCTATCTCCCTGAAGTTGCAGCAGAGCAGACAGAAG
66 TTGCAGAGAGCAGATCGCATCCAGTCCTATCTCCCTAAAGTTGCAGCGGAGCAGACAGAAG
* * * * * *
53178020 AAAATAATCATATCTCTCTAAAGTTTCAGTGGAGTGAATTAAAAAT-AGATCTTATCTCTCTAAA
1 AAAATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATT-AAAATCAGATCTTATCTCTCTAAA
* * * * *
53178084 GTTGCAAAGAACAGATCACATCCAGTCCTATCTCCCTAAAGTTGCAGCGGAGCAGGCTGAA-
65 GTTGCAGAGAGCAGATCGCATCCAGTCCTATCTCCCTAAAGTTGCAGCGGAGCAGACAGAAG
* *
53178145 AAAATCAATCCTATCTCCCTGAAGTTGCAGTGGAGC-GATTAAAACCGCAGATCTTATCTCTCTG
1 AAAAT-AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAA--TCAGATCTTATCTCTCTA
*
53178209 AAGTTGCAGTATAGCAGATCGCATC
63 AAGTTGCAG-AGAGCAGATCGCATC
53178234 AGACTTATTT
Statistics
Matches: 529, Mismatches: 56, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
124 4 0.01
125 115 0.22
126 375 0.71
127 23 0.04
128 12 0.02
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (126 bp):
AAAATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTAAAG
TTGCAGAGAGCAGATCGCATCCAGTCCTATCTCCCTAAAGTTGCAGCGGAGCAGACAGAAG
Found at i:53178078 original size:251 final size:250
Alignment explanation
Indices: 53177517--53178233 Score: 1069
Period size: 251 Copynumber: 2.8 Consensus size: 250
53177507 CAAATTGAAA
53177517 AAAATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTAAAG
1 AAAATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTAAAG
* * * *
53177582 TTGCAGAGAACAGATTGCATCCAGTCCTATCTCCCTGAAGTTACAGCGGAGCAGACATAAGAAAA
66 TTGCAGAGAACAGATCGCATCCAGTCCTATCTCCCTAAAGTTGCAGCGGAGCAGACAGAAGAAAA
53177647 TAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCAGATCTTATCTCTCTGAAGTTGC
131 TAATCCTATCTCCCTGAAGTTGCAGTGGAGC-GATTAAAAT-AGATCTTATCTCTCTGAAGTTGC
* * * *
53177712 AGAGAGCAGATCGCATCCAGTCCTATCTCTCTAAAGTTATAGCGGAGCAAATAGAAG
194 AGAGAGCAGATCGCATCCAGTCCTATCTCCCTAAAGTTACAGCAGAGCAAACAGAAG
* *
53177769 AAAATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATATTATCTCTCTAAAT
1 AAAATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTAAAG
* * * *
53177834 TTACAGAGAGCAGATCGCATCCAGTCTTATCTCCCTAAAGTTGCAGCAGAGCAGACAGAAGAAAA
66 TTGCAGAGAACAGATCGCATCCAGTCCTATCTCCCTAAAGTTGCAGCGGAGCAGACAGAAGAAAA
*
53177899 TAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATAGATCTTATCTTTCTGAAGTTGCA
131 TAATCCTATCTCCCTGAAGTTGCAGTGGAGC-GATTAAAATAGATCTTATCTCTCTGAAGTTGCA
* * *
53177964 GAGAGCAGATCGCATCCAGTCCTATCTCCCTGAAGTTGCAGCAGAGCAGACAGAAG
195 GAGAGCAGATCGCATCCAGTCCTATCTCCCTAAAGTTACAGCAGAGCAAACAGAAG
* * * * * *
53178020 AAAATAATCATATCTCTCTAAAGTTTCAGTGGAGTGAATTAAAAAT-AGATCTTATCTCTCTAAA
1 AAAATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATT-AAAATCAGATCTTATCTCTCTAAA
* * * *
53178084 GTTGCAAAGAACAGATCACATCCAGTCCTATCTCCCTAAAGTTGCAGCGGAGCAGGCTGAA-AAA
65 GTTGCAGAGAACAGATCGCATCCAGTCCTATCTCCCTAAAGTTGCAGCGGAGCAGACAGAAGAAA
*
53178148 ATCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGATTAAAACCGCAGATCTTATCTCTCTGAAGT
130 AT-AATCCTATCTCCCTGAAGTTGCAGTGGAGCGATTAAAA---TAGATCTTATCTCTCTGAAGT
*
53178213 TGCAGTATAGCAGATCGCATC
191 TGCAG-AGAGCAGATCGCATC
53178234 AGACTTATTT
Statistics
Matches: 421, Mismatches: 38, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
250 13 0.03
251 205 0.49
252 165 0.39
253 24 0.06
254 14 0.03
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (250 bp):
AAAATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTAAAG
TTGCAGAGAACAGATCGCATCCAGTCCTATCTCCCTAAAGTTGCAGCGGAGCAGACAGAAGAAAA
TAATCCTATCTCCCTGAAGTTGCAGTGGAGCGATTAAAATAGATCTTATCTCTCTGAAGTTGCAG
AGAGCAGATCGCATCCAGTCCTATCTCCCTAAAGTTACAGCAGAGCAAACAGAAG
Found at i:53179338 original size:3 final size:3
Alignment explanation
Indices: 53179332--53179377 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
53179322 TTTATATATA
*
53179332 TAT TAT TAAT T-T TAT TA- TAT TAAT TAT TAT TGT TAT TAT TAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT
53179377 T
1 T
53179378 TCAATACATA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
2 4 0.11
3 27 0.73
4 6 0.16
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:53179350 original size:21 final size:20
Alignment explanation
Indices: 53179318--53179375 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 20
53179308 CATCTGTTGT
*
53179318 TTTTTTTATATATATATTATTAA
1 TTTTATTATAT-TA-ATTATT-A
53179341 TTTTATTATATTAATTATTA
1 TTTTATTATATTAATTATTA
53179361 TTGTTATTATTATTA
1 TT-TTATTA-TATTA
53179376 TTTCAATACA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 3 0.09
21 12 0.38
22 7 0.22
23 10 0.31
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (20 bp):
TTTTATTATATTAATTATTA
Found at i:53190398 original size:42 final size:42
Alignment explanation
Indices: 53190346--53190444 Score: 117
Period size: 42 Copynumber: 2.4 Consensus size: 42
53190336 TACTTCAATT
* * * * *
53190346 TATCCGATGATGCATTTATGTGTCAGTATAACTACTTTGGTA
1 TATCCAATGATACACTTATATGCCAGTATAACTACTTTGGTA
** *
53190388 TATCCAATGATACACTTATATGCCAGTATATTTGCTTTGGTA
1 TATCCAATGATACACTTATATGCCAGTATAACTACTTTGGTA
*
53190430 TATTCAATGATACAC
1 TATCCAATGATACAC
53190445 GTACGTGCTA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.39
Consensus pattern (42 bp):
TATCCAATGATACACTTATATGCCAGTATAACTACTTTGGTA
Found at i:53190458 original size:42 final size:42
Alignment explanation
Indices: 53190380--53190473 Score: 134
Period size: 42 Copynumber: 2.2 Consensus size: 42
53190370 AGTATAACTA
* *
53190380 CTTTGGTATATCCAATGATACACTTATATGCCAGTATATTTG
1 CTTTGGTATATCCAATGATACACGTACATGCCAGTATATTTG
* * *
53190422 CTTTGGTATATTCAATGATACACGTACGTGCTAGTATATTTG
1 CTTTGGTATATCCAATGATACACGTACATGCCAGTATATTTG
*
53190464 CTTTAGTATA
1 CTTTGGTATA
53190474 CCAGATTATT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.41
Consensus pattern (42 bp):
CTTTGGTATATCCAATGATACACGTACATGCCAGTATATTTG
Found at i:53191989 original size:25 final size:26
Alignment explanation
Indices: 53191947--53192063 Score: 109
Period size: 25 Copynumber: 4.7 Consensus size: 26
53191937 AGCATGTAAA
* **
53191947 CGGGAAGCTCTTCCGAGCCATATAA-
1 CGGGAAGCTCATGAGAGCCATATAAT
* *
53191972 CAGGAAGCTCATGAGAGCCGTA-AAT
1 CGGGAAGCTCATGAGAGCCATATAAT
* * *
53191997 CGGGTAGCTCAAGAGAGCTAT-TAAT
1 CGGGAAGCTCATGAGAGCCATATAAT
*
53192022 CGGGAAGCTCAT-ACGAGCCAAAT-AT
1 CGGGAAGCTCATGA-GAGCCATATAAT
53192047 CGGGAAGCTCATGAGAG
1 CGGGAAGCTCATGAGAG
53192064 TTGTGGTGTG
Statistics
Matches: 73, Mismatches: 14, Indels: 10
0.75 0.14 0.10
Matches are distributed among these distances:
24 3 0.04
25 68 0.93
26 2 0.03
ACGTcount: A:0.32, C:0.21, G:0.28, T:0.18
Consensus pattern (26 bp):
CGGGAAGCTCATGAGAGCCATATAAT
Found at i:53198905 original size:2 final size:2
Alignment explanation
Indices: 53198898--53198950 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
53198888 TTAAACATTA
53198898 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53198940 AT AT AT AT AT A
1 AT AT AT AT AT A
53198951 CGACATTAAC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:53201695 original size:13 final size:13
Alignment explanation
Indices: 53201677--53201701 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53201667 ACAAACGAGA
53201677 AAATTTTCACACG
1 AAATTTTCACACG
53201690 AAATTTTCACAC
1 AAATTTTCACAC
53201702 TTATCAATTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:53204563 original size:25 final size:24
Alignment explanation
Indices: 53204535--53204650 Score: 94
Period size: 25 Copynumber: 4.7 Consensus size: 24
53204525 GCATGTAAAT
*
53204535 GGGAAGCTCATGCGAGCTAAGCATC
1 GGGAAGCTCATGAGAGCTAAG-ATC
53204560 GGGAAGCTCATGAGAGCCGTAAG-TC
1 GGGAAGCTCATGAGAG-C-TAAGATC
* * *
53204585 GAGTAGCTCAAGAGAGCTATTA-ATC
1 GGGAAGCTCATGAGAGCTA--AGATC
* *
53204610 GGGAAGCTCAT-ACGAGCCAAATATC
1 GGGAAGCTCATGA-GAG-CTAAGATC
53204635 GGGAAGCTCATGAGAG
1 GGGAAGCTCATGAGAG
53204651 TTGTGGTGTG
Statistics
Matches: 74, Mismatches: 8, Indels: 18
0.74 0.08 0.18
Matches are distributed among these distances:
23 2 0.03
24 3 0.04
25 61 0.82
26 4 0.05
27 4 0.05
ACGTcount: A:0.32, C:0.20, G:0.31, T:0.17
Consensus pattern (24 bp):
GGGAAGCTCATGAGAGCTAAGATC
Found at i:53207973 original size:36 final size:36
Alignment explanation
Indices: 53207933--53208005 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
53207923 TAATTGAGTT
53207933 AATTTATTCAATGAGGAATTAAATTAAGCAGTCGTA
1 AATTTATTCAATGAGGAATTAAATTAAGCAGTCGTA
53207969 AATTTATTCAATGAGGAATTAAATTAAGCAGTCGTA
1 AATTTATTCAATGAGGAATTAAATTAAGCAGTCGTA
53208005 A
1 A
53208006 GAATTGTTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.33
Consensus pattern (36 bp):
AATTTATTCAATGAGGAATTAAATTAAGCAGTCGTA
Found at i:53214374 original size:124 final size:124
Alignment explanation
Indices: 53214031--53214401 Score: 582
Period size: 123 Copynumber: 3.0 Consensus size: 124
53214021 TTAGGGTTTT
* *** * *
53214031 TAGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGATCAAATAGTATAAAATCGCTTCTAGT
1 TAGGTCATGGAAGAAATAATTT-TTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
53214096 TGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
65 TGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
*
53214156 TAGGTCATGGAAGAAAT-ATTTTTTTTGACGTTTCTGAGGAAATAGTATAAAATCGCTTCTAGCT
1 TAGGTCATGGAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCT
* * * *
53214220 GGATGCTATTTGAGAAGAATTTGTGAAATCGCGTCCTCATGGACGCGATTTTGCTACTG
66 GGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
* * *
53214279 TTGGTCATGGAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATTAAATCGCTTCTAGCA
1 TAGGTCATGGAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCT
* *
53214344 AGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTTGTGGACGCGCTTTTGCTACA
66 GGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACA
53214402 ATAGCATGTT
Statistics
Matches: 224, Mismatches: 21, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
123 108 0.48
124 100 0.45
125 16 0.07
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.34
Consensus pattern (124 bp):
TAGGTCATGGAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCT
GGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
Found at i:53216650 original size:28 final size:27
Alignment explanation
Indices: 53216617--53216715 Score: 119
Period size: 28 Copynumber: 3.6 Consensus size: 27
53216607 TAATGAGATT
53216617 AGCACTAAGTGTGCGAGTTTAATTGAA
1 AGCACTAAGTGTGCGAGTTTAATTGAA
* **
53216644 ATGCACTAAGTGTGCGAGTATAAGGGTAA
1 A-GCACTAAGTGTGCGAGTTTAATTG-AA
*
53216673 AGCACTAAGTGTGCGAGTTTGATT-ATTA
1 AGCACTAAGTGTGCGAGTTTAATTGA--A
53216701 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
53216716 TACTTATTAA
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
26 1 0.02
27 1 0.02
28 56 0.92
29 3 0.05
ACGTcount: A:0.31, C:0.12, G:0.28, T:0.28
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTTAATTGAA
Found at i:53217760 original size:47 final size:46
Alignment explanation
Indices: 53217648--53217764 Score: 137
Period size: 47 Copynumber: 2.5 Consensus size: 46
53217638 TTTTGTTATA
* * * *
53217648 AATTTAATGTATAATGCTGTCCAATTTTGAGTATATTTAAGCTGTCT
1 AATTTGATGTATAATGCTGTCC-ATTTAGAGCATATTTAAGCTGTCC
* *
53217695 AATTCGATGTATAATGCTGTCCATTTAGAGCATA-TTATTGCTGTCC
1 AATTTGATGTATAATGCTGTCCATTTAGAGCATATTTA-AGCTGTCC
*
53217741 AATTTGATGAATAATTGCTGTCCA
1 AATTTGATGTATAA-TGCTGTCCA
53217765 AAACAGGGTT
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
45 3 0.05
46 28 0.47
47 29 0.48
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (46 bp):
AATTTGATGTATAATGCTGTCCATTTAGAGCATATTTAAGCTGTCC
Found at i:53217761 original size:23 final size:23
Alignment explanation
Indices: 53217648--53217765 Score: 93
Period size: 23 Copynumber: 5.1 Consensus size: 23
53217638 TTTTGTTATA
*
53217648 AATTTAATGTATAA-TGCTGTCC
1 AATTTGATGTATAATTGCTGTCC
* *
53217670 AATTTTGA-GTATATTTAAGCTGTCT
1 AA-TTTGATGTATAATT--GCTGTCC
*
53217695 AATTCGATGTATAA-TGCTGTCC
1 AATTTGATGTATAATTGCTGTCC
*
53217717 -ATTTAGA-GCATATTATTGCTGTCC
1 AATTT-GATG--TATAATTGCTGTCC
*
53217741 AATTTGATGAATAATTGCTGTCC
1 AATTTGATGTATAATTGCTGTCC
53217764 AA
1 AA
53217766 AACAGGGTTG
Statistics
Matches: 75, Mismatches: 10, Indels: 21
0.71 0.09 0.20
Matches are distributed among these distances:
21 4 0.05
22 15 0.20
23 23 0.31
24 15 0.20
25 18 0.24
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.41
Consensus pattern (23 bp):
AATTTGATGTATAATTGCTGTCC
Found at i:53220242 original size:25 final size:25
Alignment explanation
Indices: 53220214--53220445 Score: 232
Period size: 25 Copynumber: 9.6 Consensus size: 25
53220204 TAGGCTCATG
53220214 TTATTACATCAAATAAACTTCTATT
1 TTATTACATCAAATAAACTTCTATT
* **
53220239 TTATTACATCAAAT-AA--TATAAA
1 TTATTACATCAAATAAACTTCTATT
** * * *
53220261 AAATAAC-TCAAAAAAATTTCTATT
1 TTATTACATCAAATAAACTTCTATT
*
53220285 TTATTACATCAATTAAACTTCTATT
1 TTATTACATCAAATAAACTTCTATT
*
53220310 TTATTACATCAAATAAACTTCAATT
1 TTATTACATCAAATAAACTTCTATT
*
53220335 TTATTACATCAAAT--A--T-TATC
1 TTATTACATCAAATAAACTTCTATT
** * * *
53220355 AAAATA-ACTCAAAAAAATTTCTATT
1 TTATTACA-TCAAATAAACTTCTATT
53220380 TTATTACATCAAATAAACTTCTATT
1 TTATTACATCAAATAAACTTCTATT
*
53220405 TTATTACATCAAATAAACTTTTATT
1 TTATTACATCAAATAAACTTCTATT
53220430 TTATTACATCAAATAA
1 TTATTACATCAAATAA
53220446 TATCATAATA
Statistics
Matches: 165, Mismatches: 31, Indels: 22
0.76 0.14 0.10
Matches are distributed among these distances:
19 1 0.01
20 10 0.06
21 6 0.04
22 10 0.06
23 1 0.01
24 10 0.06
25 126 0.76
26 1 0.01
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (25 bp):
TTATTACATCAAATAAACTTCTATT
Found at i:53220400 original size:95 final size:95
Alignment explanation
Indices: 53220214--53220491 Score: 475
Period size: 95 Copynumber: 2.9 Consensus size: 95
53220204 TAGGCTCATG
*
53220214 TTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATAAAAAATAACTCAAAAAAATT
1 TTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATAT-CAAAATAACTCAAAAAAATT
*
53220279 TCTATTTTATTACATCAATTAAACTTCTATT
65 TCTATTTTATTACATCAAATAAACTTCTATT
* *
53220310 TTATTACATCAAATAAACTTCAATTTTATTACATCAAATATTATCAAAATAACTCAAAAAAATTT
1 TTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAAATTT
53220375 CTATTTTATTACATCAAATAAACTTCTATT
66 CTATTTTATTACATCAAATAAACTTCTATT
* * *
53220405 TTATTACATCAAATAAACTTTTATTTTATTACATCAAATAATATCATAATAACTCAAAAAAATTG
1 TTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAAATTT
*
53220470 CTATTTTATTACATAAAATAAA
66 CTATTTTATTACATCAAATAAA
53220492 ATTAAAATAT
Statistics
Matches: 172, Mismatches: 10, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
95 130 0.76
96 42 0.24
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.40
Consensus pattern (95 bp):
TTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAAATTT
CTATTTTATTACATCAAATAAACTTCTATT
Found at i:53221608 original size:7 final size:7
Alignment explanation
Indices: 53221598--53221622 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
53221588 TTATATACAT
53221598 AATACTA
1 AATACTA
53221605 AATACTA
1 AATACTA
53221612 AATACTA
1 AATACTA
53221619 AATA
1 AATA
53221623 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:53222661 original size:11 final size:11
Alignment explanation
Indices: 53222647--53222724 Score: 72
Period size: 11 Copynumber: 7.0 Consensus size: 11
53222637 TTAAATATGG
53222647 ATTTGAGAGAA
1 ATTTGAGAGAA
*
53222658 ATTTTGA-AGGA
1 A-TTTGAGAGAA
*
53222669 ATTTGAGAGCA
1 ATTTGAGAGAA
*
53222680 AGTTGAGAGGAA
1 ATTTGAGA-GAA
53222692 A-TTGAGAGGAA
1 ATTTGAGA-GAA
53222703 A-TTGAGAAGAA
1 ATTTGAG-AGAA
53222714 ATTTGAGAGAA
1 ATTTGAGAGAA
53222725 GATTAGTTTG
Statistics
Matches: 58, Mismatches: 4, Indels: 10
0.81 0.06 0.14
Matches are distributed among these distances:
10 5 0.09
11 39 0.67
12 14 0.24
ACGTcount: A:0.44, C:0.01, G:0.31, T:0.24
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:53222686 original size:33 final size:33
Alignment explanation
Indices: 53222649--53222724 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 33
53222639 AAATATGGAT
* *
53222649 TTGAGAGAAATTTTGA-AGGAATTTGAG-AGCAAG
1 TTGAGAGAAA--TTGAGAGGAAATTGAGAAGAAAG
*
53222682 TTGAGAGGAAATTGAGAGGAAATTGAGAAGAAAT
1 TTGAGA-GAAATTGAGAGGAAATTGAGAAGAAAG
53222716 TTGAGAGAA
1 TTGAGAGAA
53222725 GATTAGTTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
32 4 0.11
33 19 0.51
34 14 0.38
ACGTcount: A:0.43, C:0.01, G:0.32, T:0.24
Consensus pattern (33 bp):
TTGAGAGAAATTGAGAGGAAATTGAGAAGAAAG
Found at i:53227196 original size:12 final size:12
Alignment explanation
Indices: 53227179--53227203 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53227169 ATTTTATAAC
53227179 ATAAATATTGTT
1 ATAAATATTGTT
53227191 ATAAATATTGTT
1 ATAAATATTGTT
53227203 A
1 A
53227204 ATAGCCTCTG
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (12 bp):
ATAAATATTGTT
Found at i:53228305 original size:31 final size:31
Alignment explanation
Indices: 53228267--53228327 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
53228257 TCGGGTTGTC
*
53228267 TAGCAACAATAACTTGCCACCCTA-GATTGCT
1 TAGCAACAATAACTTACCA-CCTAGGATTGCT
* *
53228298 TAGCAACATTGACTTACCACCTAGGATTGC
1 TAGCAACAATAACTTACCACCTAGGATTGC
53228328 CCGACAACGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (31 bp):
TAGCAACAATAACTTACCACCTAGGATTGCT
Found at i:53241212 original size:48 final size:48
Alignment explanation
Indices: 53241160--53241256 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
53241150 GAGGAAAAAG
53241160 TTAAAAAAATTGAATACATCCATGTATGACCTATATCATGTCCAATGC
1 TTAAAAAAATTGAATACATCCATGTATGACCTATATCATGTCCAATGC
53241208 TTAAAAAAATTGAATACATCCATGTATGACCTATATCATGTCCAATGC
1 TTAAAAAAATTGAATACATCCATGTATGACCTATATCATGTCCAATGC
53241256 T
1 T
53241257 CCTGAGCCTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (48 bp):
TTAAAAAAATTGAATACATCCATGTATGACCTATATCATGTCCAATGC
Found at i:53244750 original size:8 final size:9
Alignment explanation
Indices: 53244722--53244755 Score: 52
Period size: 10 Copynumber: 3.8 Consensus size: 9
53244712 CCTTAAGAGT
53244722 TTTATTTTA
1 TTTATTTTA
53244731 TTTTATTTTA
1 -TTTATTTTA
53244741 TTTA-TTTA
1 TTTATTTTA
53244749 TTTATTT
1 TTTATTT
53244756 CACTGCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.35
9 6 0.26
10 9 0.39
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTATTTTA
Found at i:53257819 original size:3 final size:3
Alignment explanation
Indices: 53257811--53257838 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
53257801 GCTTAAGTCT
53257811 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
53257839 AAGTGAGTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:53258064 original size:20 final size:20
Alignment explanation
Indices: 53258027--53258064 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
53258017 TAGAACTTTT
*
53258027 TAATTTATTTATGTTATTAA
1 TAATTTATTTATGATATTAA
53258047 TAATTATATTTAT-ATATT
1 TAATT-TATTTATGATATT
53258065 TTTCAACTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (20 bp):
TAATTTATTTATGATATTAA
Found at i:53258871 original size:88 final size:87
Alignment explanation
Indices: 53258711--53258881 Score: 191
Period size: 88 Copynumber: 2.0 Consensus size: 87
53258701 ATAAAAAATT
* * * ** * * *
53258711 CTCAAAATTTTTCAAAAAAAGTAATTAAGTCTCTACTTTTTTTTGCACTCGTTTATGTACTTAAA
1 CTCAAAATTTTTCAAAAAAAGCAATTAAGCCTCTACTATTTTTTGCACTCAATTAGGCAATTAAA
* *
53258776 CTTTCAAAATGCATCAAAAGTCC
66 CTGTC-AAATGCATAAAAAGTCC
* * * *
53258799 CTCAAACTTTTTTAAAAAAAGCAATTAAGCCTCTGA-TATTTTTTGTACTCAATTAGGCAATTGA
1 CTCAAAATTTTTCAAAAAAAGCAATTAAGCCTCT-ACTATTTTTTGCACTCAATTAGGCAATTAA
53258863 ACTGTCAAATGCATAAAAA
65 ACTGTCAAATGCATAAAAA
53258882 ATACCCTTTG
Statistics
Matches: 68, Mismatches: 14, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
87 12 0.18
88 55 0.81
89 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.36
Consensus pattern (87 bp):
CTCAAAATTTTTCAAAAAAAGCAATTAAGCCTCTACTATTTTTTGCACTCAATTAGGCAATTAAA
CTGTCAAATGCATAAAAAGTCC
Found at i:53259304 original size:10 final size:9
Alignment explanation
Indices: 53259289--53259409 Score: 68
Period size: 9 Copynumber: 12.9 Consensus size: 9
53259279 AGTACGATCA
53259289 TTTTTATAT
1 TTTTTATAT
*
53259298 TTTTT-TACGA
1 TTTTTATA--T
53259308 TTTTTATAT
1 TTTTTATAT
*
53259317 TTCTTTACAT
1 TT-TTTATAT
*
53259327 TTTTTATAA
1 TTTTTATAT
53259336 TTTTTATGAT
1 TTTTTAT-AT
*
53259346 TTTATA-ATT
1 TTTTTATA-T
*
53259355 TTTTTCTAAT
1 TTTTTAT-AT
*
53259365 TTTTAATAT
1 TTTTTATAT
53259374 TTTTTATAGT
1 TTTTTATA-T
*
53259384 TTCTTT-TAA
1 TT-TTTATAT
* *
53259393 ATTTAATAT
1 TTTTTATAT
53259402 TTTTTATA
1 TTTTTATA
53259410 ACTTATATTG
Statistics
Matches: 83, Mismatches: 18, Indels: 22
0.67 0.15 0.18
Matches are distributed among these distances:
8 5 0.06
9 42 0.51
10 30 0.36
11 6 0.07
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (9 bp):
TTTTTATAT
Found at i:53259312 original size:19 final size:19
Alignment explanation
Indices: 53259288--53259378 Score: 82
Period size: 19 Copynumber: 4.8 Consensus size: 19
53259278 TAGTACGATC
53259288 ATTTTTATATTTTTTTACG
1 ATTTTTATATTTTTTTACG
*
53259307 ATTTTTATATTTCTTTAC-
1 ATTTTTATATTTTTTTACG
* *
53259325 ATTTTT-TATAATTTTTATG
1 ATTTTTATAT-TTTTTTACG
*
53259344 A-TTTTATAATTTTTTT-CTA
1 ATTTTTAT-ATTTTTTTAC-G
53259363 ATTTTTAATATTTTTT
1 ATTTTT-ATATTTTTT
53259379 ATAGTTTCTT
Statistics
Matches: 58, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
17 3 0.05
18 15 0.26
19 25 0.43
20 13 0.22
21 2 0.03
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.69
Consensus pattern (19 bp):
ATTTTTATATTTTTTTACG
Found at i:53259328 original size:37 final size:36
Alignment explanation
Indices: 53259287--53259378 Score: 89
Period size: 37 Copynumber: 2.4 Consensus size: 36
53259277 TTAGTACGAT
53259287 CATTTTTATATTTTTTTACGATTTT-TATATTTCTTTA
1 CATTTTTATATTTTTTTACGATTTTATA-ATTT-TTTA
* * *
53259324 CATTTTT-TATAATTTTTATGATTTTATAATTTTTTT
1 CATTTTTATAT-TTTTTTACGATTTTATAATTTTTTA
53259360 CTAATTTTTAATATTTTTT
1 C--ATTTTT-ATATTTTTT
53259379 ATAGTTTCTT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
36 7 0.16
37 23 0.51
38 8 0.18
39 4 0.09
40 3 0.07
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.68
Consensus pattern (36 bp):
CATTTTTATATTTTTTTACGATTTTATAATTTTTTA
Found at i:53259338 original size:28 final size:27
Alignment explanation
Indices: 53259289--53259407 Score: 100
Period size: 28 Copynumber: 4.2 Consensus size: 27
53259279 AGTACGATCA
**
53259289 TTTTTATATTTTTTTACGATTTTTATAT
1 TTTTTA-ATTTTTTTATAATTTTTATAT
53259317 TTCTTTACA-TTTTTTATAATTTTTATGAT
1 TT-TTTA-ATTTTTTTATAATTTTTAT-AT
* *
53259346 TTTATAATTTTTTTCTAATTTTTAATAT
1 TTTTTAATTTTTTTATAATTTTT-ATAT
*
53259374 TTTTTATAGTTTCTTTTA-AA-TTTAATAT
1 TTTTTA-A-TTT-TTTTATAATTTTTATAT
53259402 TTTTTA
1 TTTTTA
53259408 TAACTTATAT
Statistics
Matches: 76, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
27 1 0.01
28 51 0.67
29 15 0.20
30 5 0.07
31 4 0.05
ACGTcount: A:0.25, C:0.04, G:0.03, T:0.68
Consensus pattern (27 bp):
TTTTTAATTTTTTTATAATTTTTATAT
Found at i:53260785 original size:45 final size:45
Alignment explanation
Indices: 53260705--53260792 Score: 124
Period size: 45 Copynumber: 2.0 Consensus size: 45
53260695 GGTCCTTGAA
* *
53260705 AAAATTAGTATAAATAATTAATAGTAACTACTATGTAATTTAAAT
1 AAAATTAGTATAAATAATTAATAATAAATACTATGTAATTTAAAT
**
53260750 AAAATTAGTATAAATAAATT-ATAATAAATTTTATGTAATTTAA
1 AAAATTAGTATAAAT-AATTAATAATAAATACTATGTAATTTAA
53260793 TTAATTATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
45 34 0.89
46 4 0.11
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (45 bp):
AAAATTAGTATAAATAATTAATAATAAATACTATGTAATTTAAAT
Found at i:53271506 original size:25 final size:25
Alignment explanation
Indices: 53271478--53271548 Score: 67
Period size: 25 Copynumber: 2.8 Consensus size: 25
53271468 CCCGATATAT
53271478 GGCTCTTCGGAGCTTCCTGATTAAA
1 GGCTCTTCGGAGCTTCCTGATTAAA
* *
53271503 GGCTCTTTGTGAGCTTCAC-G-TTAAT
1 GGCTCTTCG-GAGCTTC-CTGATTAAA
*
53271528 GGCT-TTCCGGAGCTTCTTGAT
1 GGCTCTT-CGGAGCTTCCTGAT
53271549 ATGGCTCGCT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
24 10 0.27
25 18 0.49
26 8 0.22
27 1 0.03
ACGTcount: A:0.15, C:0.23, G:0.25, T:0.37
Consensus pattern (25 bp):
GGCTCTTCGGAGCTTCCTGATTAAA
Found at i:53271653 original size:24 final size:24
Alignment explanation
Indices: 53271610--53271671 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
53271600 TAGCTCTTCG
* *
53271610 GAGCTACCTGTTATTGGCTCGCAT
1 GAGCTTCCCGTTATTGGCTCGCAT
* **
53271634 GAGCTTTCCGATTATT-GCTCTTAT
1 GAGCTTCCCG-TTATTGGCTCGCAT
53271658 GAGCTTCCCGTTAT
1 GAGCTTCCCGTTAT
53271672 ACAGCCCAGA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
23 4 0.13
24 22 0.71
25 5 0.16
ACGTcount: A:0.16, C:0.24, G:0.21, T:0.39
Consensus pattern (24 bp):
GAGCTTCCCGTTATTGGCTCGCAT
Found at i:53272680 original size:14 final size:14
Alignment explanation
Indices: 53272661--53272689 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
53272651 GCAGAGACAC
53272661 GGGCGTGTGTCTCA
1 GGGCGTGTGTCTCA
53272675 GGGCGTGTGTCTCA
1 GGGCGTGTGTCTCA
53272689 G
1 G
53272690 CCGTGTGTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.21, G:0.45, T:0.28
Consensus pattern (14 bp):
GGGCGTGTGTCTCA
Found at i:53277127 original size:34 final size:34
Alignment explanation
Indices: 53277084--53277149 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 34
53277074 AGTAAAATAT
*
53277084 TTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTCCGTAAAATGATTTACTGGAAAATATTTTAC
53277117 TTTCCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTCC-GTAAAATGATTTACTGGAAAATATTTT
53277150 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 5 0.17
34 12 0.40
35 13 0.43
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.44
Consensus pattern (34 bp):
TTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:53281010 original size:33 final size:35
Alignment explanation
Indices: 53280973--53281069 Score: 89
Period size: 33 Copynumber: 2.8 Consensus size: 35
53280963 ATGGTTATAT
53280973 TTAAATATTTAAAATATAATTTATATATT-C-TAA
1 TTAAATATTTAAAATATAATTTATATATTGCTTAA
* *
53281006 TTAAAT-TTTATAA-ATAATTAATATTTATTGCTTAA
1 TTAAATATTTAAAATATAATT--TATATATTGCTTAA
*
53281041 --AAATATTTAAAATTTATATTTCATATATT
1 TTAAATATTTAAAATATA-ATTT-ATATATT
53281070 AAAATATTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
31 6 0.12
32 6 0.12
33 17 0.33
34 8 0.16
35 11 0.22
36 3 0.06
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (35 bp):
TTAAATATTTAAAATATAATTTATATATTGCTTAA
Found at i:53283602 original size:18 final size:18
Alignment explanation
Indices: 53283581--53283615 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
53283571 TAAAAAATTA
53283581 TAAAAAACATAAAAAACG
1 TAAAAAACATAAAAAACG
* *
53283599 TAAAAAAGATGAAAAAC
1 TAAAAAACATAAAAAAC
53283616 AAAAAGAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.71, C:0.09, G:0.09, T:0.11
Consensus pattern (18 bp):
TAAAAAACATAAAAAACG
Found at i:53294054 original size:15 final size:16
Alignment explanation
Indices: 53294034--53294063 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
53294024 GACTCTTTGA
53294034 TTACAAAAG-GAAAAT
1 TTACAAAAGAGAAAAT
53294049 TTACAAAAGAGAAAA
1 TTACAAAAGAGAAAA
53294064 CTAAAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.63, C:0.07, G:0.13, T:0.17
Consensus pattern (16 bp):
TTACAAAAGAGAAAAT
Found at i:53298762 original size:6 final size:7
Alignment explanation
Indices: 53298746--53298771 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
53298736 GGGTAAATTA
53298746 TTTTTCT
1 TTTTTCT
53298753 TTTTTCT
1 TTTTTCT
53298760 TTTTTCT
1 TTTTTCT
53298767 TTTTT
1 TTTTT
53298772 TTAAAGGACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTCT
Found at i:53301527 original size:25 final size:25
Alignment explanation
Indices: 53301499--53301547 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
53301489 TATGGCTCGA
53301499 ATGACCTTCCCGTTACATGACTCAC
1 ATGACCTTCCCGTTACATGACTCAC
** *
53301524 ATGAGTTTCCCGTTATATGACTCA
1 ATGACCTTCCCGTTACATGACTCA
53301548 AAAAAGCTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.24, C:0.29, G:0.14, T:0.33
Consensus pattern (25 bp):
ATGACCTTCCCGTTACATGACTCAC
Found at i:53301558 original size:25 final size:25
Alignment explanation
Indices: 53301504--53301562 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
53301494 CTCGAATGAC
* **
53301504 CTTCCCGTTACATGACTCACATGAG
1 CTTCCCGTTACATGACTCAAAAAAG
* *
53301529 TTTCCCGTTATATGACTCAAAAAAG
1 CTTCCCGTTACATGACTCAAAAAAG
53301554 CTTCCCGTT
1 CTTCCCGTT
53301563 TTCATGTTTG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.25, C:0.29, G:0.14, T:0.32
Consensus pattern (25 bp):
CTTCCCGTTACATGACTCAAAAAAG
Found at i:53316437 original size:6 final size:6
Alignment explanation
Indices: 53316426--53316460 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
53316416 CCCTAAACCC
*
53316426 CAAACT CAAACT CAAACC CAAACT CAAACT CAAAC
1 CAAACT CAAACT CAAACT CAAACT CAAACT CAAAC
53316461 CTCAGGCCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.51, C:0.37, G:0.00, T:0.11
Consensus pattern (6 bp):
CAAACT
Found at i:53316447 original size:18 final size:18
Alignment explanation
Indices: 53316424--53316461 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
53316414 CACCCTAAAC
53316424 CCCAAACTCAAACTCAAA
1 CCCAAACTCAAACTCAAA
53316442 CCCAAACTCAAACTCAAA
1 CCCAAACTCAAACTCAAA
53316460 CC
1 CC
53316462 TCAGGCCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.42, G:0.00, T:0.11
Consensus pattern (18 bp):
CCCAAACTCAAACTCAAA
Found at i:53319791 original size:42 final size:41
Alignment explanation
Indices: 53319743--53319875 Score: 144
Period size: 42 Copynumber: 3.2 Consensus size: 41
53319733 AAGGCTGAAT
* *
53319743 AGAAGCTCATGAGAGCTAAACAGAAACCCATAAGGGTTGAA-
1 AGAAGCTCAT-AGAGCTAAACGGAAACCCATAAGGGTTAAAC
* * *
53319784 TGAAAGCTCGCA-AGAGCTGAACGGAAACCTATAAGGGTTAAAC
1 AG-AAGCT--CATAGAGCTAAACGGAAACCCATAAGGGTTAAAC
* *
53319827 AGAAGCTCAATAGAGCTAAACGGAAACTCATAAGGGTTAAAT
1 AGAAGCTC-ATAGAGCTAAACGGAAACCCATAAGGGTTAAAC
53319869 AGAAGCT
1 AGAAGCT
53319876 TAGTTGAACT
Statistics
Matches: 76, Mismatches: 10, Indels: 11
0.78 0.10 0.11
Matches are distributed among these distances:
40 1 0.01
41 2 0.03
42 70 0.92
43 1 0.01
44 2 0.03
ACGTcount: A:0.43, C:0.17, G:0.24, T:0.17
Consensus pattern (41 bp):
AGAAGCTCATAGAGCTAAACGGAAACCCATAAGGGTTAAAC
Found at i:53319856 original size:21 final size:22
Alignment explanation
Indices: 53319795--53319860 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 22
53319785 GAAAGCTCGC
* *
53319795 AAGAGCTGAACGGAAAC-CTAT
1 AAGAGCTAAACGGAAACTCAAT
* * * *
53319816 AAGGGTTAAACAGAAGCTCAAT
1 AAGAGCTAAACGGAAACTCAAT
53319838 -AGAGCTAAACGGAAACTC-AT
1 AAGAGCTAAACGGAAACTCAAT
53319858 AAG
1 AAG
53319861 GGTTAAATAG
Statistics
Matches: 33, Mismatches: 10, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
20 2 0.06
21 28 0.85
22 3 0.09
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (22 bp):
AAGAGCTAAACGGAAACTCAAT
Found at i:53319867 original size:21 final size:21
Alignment explanation
Indices: 53319803--53319867 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
53319793 GCAAGAGCTG
53319803 AACGGAAAC-CTATAAGGGTTA
1 AACGGAAACTC-ATAAGGGTTA
* * * *
53319824 AACAGAAGCTCA-ATAGAGCTA
1 AACGGAAACTCATA-AGGGTTA
53319845 AACGGAAACTCATAAGGGTTA
1 AACGGAAACTCATAAGGGTTA
53319866 AA
1 AA
53319868 TAGAAGCTTA
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
20 1 0.03
21 30 0.91
22 2 0.06
ACGTcount: A:0.46, C:0.15, G:0.22, T:0.17
Consensus pattern (21 bp):
AACGGAAACTCATAAGGGTTA
Found at i:53319891 original size:42 final size:42
Alignment explanation
Indices: 53319800--53319894 Score: 120
Period size: 42 Copynumber: 2.3 Consensus size: 42
53319790 CTCGCAAGAG
*
53319800 CTGAACGGAAACCTATAAGGGTTAAACAGAAGCTCAATAGAG
1 CTGAACGGAAACCTATAAGGGTTAAACAGAAGCTCAATAGAA
* * * * *
53319842 CTAAACGGAAA-CTCATAAGGGTTAAATAGAAGCTTAGTTGAA
1 CTGAACGGAAACCT-ATAAGGGTTAAACAGAAGCTCAATAGAA
53319884 CTGAACGGAAA
1 CTGAACGGAAA
53319895 GTAAACACGA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 2 0.04
42 43 0.96
ACGTcount: A:0.43, C:0.15, G:0.23, T:0.19
Consensus pattern (42 bp):
CTGAACGGAAACCTATAAGGGTTAAACAGAAGCTCAATAGAA
Found at i:53321991 original size:22 final size:21
Alignment explanation
Indices: 53321966--53322026 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 21
53321956 ACATATAGCC
53321966 CCAAAACTTAAAACCTTAAAAA
1 CCAAAAC-TAAAACCTTAAAAA
*
53321988 CCAAATCAC-AAAACCCT-AAAA
1 CCAAA--ACTAAAACCTTAAAAA
*
53322009 CTCAACACTAAAACCTTA
1 C-CAAAACTAAAACCTTA
53322027 CACCCTAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
20 2 0.06
21 12 0.39
22 15 0.48
24 2 0.06
ACGTcount: A:0.54, C:0.30, G:0.00, T:0.16
Consensus pattern (21 bp):
CCAAAACTAAAACCTTAAAAA
Found at i:53323194 original size:40 final size:40
Alignment explanation
Indices: 53323140--53323320 Score: 326
Period size: 40 Copynumber: 4.5 Consensus size: 40
53323130 TGATTCCGTA
* * *
53323140 CACCGACATGAAGCCTGCTAGATGTATAGTCTGAATATTT
1 CACCGGCATTAAGCCTGCTAGACGTATAGTCTGAATATTT
53323180 CACCGGCATTAAGCCTGCTAGACGTATAGTCTGAATATTT
1 CACCGGCATTAAGCCTGCTAGACGTATAGTCTGAATATTT
*
53323220 CACCGGCATTAAGCCTGCTAGACGTATAATCTGAATATTT
1 CACCGGCATTAAGCCTGCTAGACGTATAGTCTGAATATTT
53323260 CACCGGCATTAAGCCTGCTAGACGTATAGTCTGAATATTT
1 CACCGGCATTAAGCCTGCTAGACGTATAGTCTGAATATTT
53323300 CACCGGCATTAAGCCTGCTAG
1 CACCGGCATTAAGCCTGCTAG
53323321 GCACAAGCCT
Statistics
Matches: 136, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 136 1.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (40 bp):
CACCGGCATTAAGCCTGCTAGACGTATAGTCTGAATATTT
Found at i:53326932 original size:6 final size:6
Alignment explanation
Indices: 53326921--53326956 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
53326911 GAAAGGAAAC
53326921 AATGAG AATGAG AATGAG AATGAG AATGAG AATGAG
1 AATGAG AATGAG AATGAG AATGAG AATGAG AATGAG
53326957 CATGGGGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.33, T:0.17
Consensus pattern (6 bp):
AATGAG
Found at i:53332786 original size:62 final size:59
Alignment explanation
Indices: 53332674--53332790 Score: 153
Period size: 62 Copynumber: 1.9 Consensus size: 59
53332664 ACCACTTTAA
* * * *
53332674 TATTAAATTAATATAATACTTATCAAGATAAATATTAGACTAAATTTAATATTAAATCT
1 TATTAAATTAATAGAATACTTATCAAGATAAACATTAAACTAAATATAATATTAAATCT
* *
53332733 TATTAAATTAATAGAATATTTATCTACAAGATAAACATTAAATTAAATATAATATTAA
1 TATTAAATTAATAGAATACTTA--T-CAAGATAAACATTAAACTAAATATAATATTAA
53332791 GATAACCACT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
59 20 0.41
61 1 0.02
62 28 0.57
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.39
Consensus pattern (59 bp):
TATTAAATTAATAGAATACTTATCAAGATAAACATTAAACTAAATATAATATTAAATCT
Found at i:53334123 original size:2 final size:2
Alignment explanation
Indices: 53334111--53334159 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
53334101 AGTTGATTGG
*
53334111 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53334153 TA TA TA T
1 TA TA TA T
53334160 GAAGCGGAGA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:53335787 original size:15 final size:16
Alignment explanation
Indices: 53335748--53335788 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
53335738 TGATTTTTGG
53335748 ATTAAA-TTGAATAGA
1 ATTAAATTTGAATAGA
* *
53335763 ATGAATTTTGAAT-GA
1 ATTAAATTTGAATAGA
53335778 ATTAAATTTGA
1 ATTAAATTTGA
53335789 TTATTTAGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.39
Consensus pattern (16 bp):
ATTAAATTTGAATAGA
Found at i:53344763 original size:15 final size:16
Alignment explanation
Indices: 53344724--53344767 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
53344714 TAAAGAAGAC
53344724 AATATTTTCATATATA
1 AATATTTTCATATATA
* *
53344740 AATTTTTTTCAT-TTTA
1 AA-TATTTTCATATATA
53344756 AATATTTTCATA
1 AATATTTTCATA
53344768 CTGTACATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 8 0.35
16 7 0.30
17 8 0.35
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (16 bp):
AATATTTTCATATATA
Found at i:53345768 original size:24 final size:24
Alignment explanation
Indices: 53345717--53345768 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
53345707 TCTAAAAATG
* * * *
53345717 TAAAAAAATTAAATATATATTTGC
1 TAAAAAAAATAAAAATATAATTCC
53345741 -AAAAAAAATAAAAATATAATTCC
1 TAAAAAAAATAAAAATATAATTCC
53345764 TAAAA
1 TAAAA
53345769 GTGTTCTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (24 bp):
TAAAAAAAATAAAAATATAATTCC
Found at i:53378554 original size:41 final size:41
Alignment explanation
Indices: 53378478--53378556 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 41
53378468 TATCTGAGAT
* *
53378478 TTTCAGGCTTAATGCCTAGCAGACTTGATGTCGGTGAATTA
1 TTTCAGACTTAATGCCTAGCAGACTTGATGCCGGTGAATTA
* * *
53378519 TTTCAGACTTTATGTCTAGCAGGCTTTG-TGCCGGTGAA
1 TTTCAGACTTAATGCCTAGCAGAC-TTGATGCCGGTGAA
53378557 ATGTATCGGG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
41 29 0.91
42 3 0.09
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (41 bp):
TTTCAGACTTAATGCCTAGCAGACTTGATGCCGGTGAATTA
Found at i:53381653 original size:12 final size:12
Alignment explanation
Indices: 53381636--53381662 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
53381626 TAGTAATTAT
53381636 ATATATATATAG
1 ATATATATATAG
53381648 ATATATATATAG
1 ATATATATATAG
53381660 ATA
1 ATA
53381663 CTTGATTAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (12 bp):
ATATATATATAG
Found at i:53383810 original size:21 final size:21
Alignment explanation
Indices: 53383786--53383842 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
53383776 ATATTTATCA
* * *
53383786 TTATACCATTATTTATTATTG
1 TTATATCATTATTTATAATGG
53383807 TTATATCATT-TATTATAATGG
1 TTATATCATTAT-TTATAATGG
53383828 TTATTATCATTATTT
1 TTA-TATCATTATTT
53383843 CTATATTCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 1 0.03
21 19 0.63
22 9 0.30
23 1 0.03
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.58
Consensus pattern (21 bp):
TTATATCATTATTTATAATGG
Found at i:53393105 original size:133 final size:133
Alignment explanation
Indices: 53392892--53393503 Score: 920
Period size: 133 Copynumber: 4.6 Consensus size: 133
53392882 TGTCTTCATG
* *
53392892 TACTGGTGGCGAAGCAGATCAAAGAAACAGATCTTGTCTCCCCATACTGGTGGTGGAATAGGTCG
1 TACTGGTGGCGAAGCAGATCAAAGAAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCG
53392957 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATACCAGATCTTGCCTTC
66 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATACCAGATCTTGCCTTC
53393022 CCA
131 CCA
*
53393025 TACTGGTGGCGAAGCAGATCAAAGAAACAGATCTTGTCTCCTCATACTGGTGGTGGAGTAGATCG
1 TACTGGTGGCGAAGCAGATCAAAGAAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCG
* *
53393090 AAGAAAACAGATCTTGTCTTTATGTACTGGCATGAAGTAGATCAAAGATACCAGATCTTGCCTTC
66 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATACCAGATCTTGCCTTC
53393155 CCA
131 CCA
* *
53393158 TACTGGTGGCGAAGCAGATCAAAGAAACAGATCTTGTCTCCCCATACTGGTAGTAGAGTAGATCG
1 TACTGGTGGCGAAGCAGATCAAAGAAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCG
* * *
53393223 AAGAAAATAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGGTACCAGATCTTGCCTTC
66 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATACCAGATCTTGCCTTC
53393288 CCA
131 CCA
53393291 TACTGGTGGCGAAGCAGATCAAAGAAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCG
1 TACTGGTGGCGAAGCAGATCAAAGAAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCG
* * * * * *
53393356 AAGAAAATAGATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGCAGGTCCTGTCTTC
66 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATACCAGATCTTGCCTTC
*
53393421 CTA
131 CCA
* ** * * * * * * * * * *
53393424 TA-TCGGTAGCGAAGTGGATCGAATATATAGATTTTATCTTCCCATACTGGTGGCGAAGTAGATT
1 TACT-GGTGGCGAAGCAGATCAAAGAAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATC
**
53393488 GAAGATTACAGATCTT
65 GAAGAAAACAGATCTT
53393504 ATCTCCCTAA
Statistics
Matches: 439, Mismatches: 39, Indels: 2
0.91 0.08 0.00
Matches are distributed among these distances:
132 1 0.00
133 438 1.00
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (133 bp):
TACTGGTGGCGAAGCAGATCAAAGAAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCG
AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATACCAGATCTTGCCTTC
CCA
Found at i:53393418 original size:89 final size:89
Alignment explanation
Indices: 53392892--53393403 Score: 419
Period size: 89 Copynumber: 5.8 Consensus size: 89
53392882 TGTCTTCATG
* * * * * *
53392892 TACTGGTGGCGAAGCAGATCAAAG-AAACAGATCTTGTCTCCCCATACTGGTGGTGGAA-TAGGT
1 TACTGGTGGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCACATACTGGTCGT-GAAGTAGAT
* * ***
53392955 CGAAGAAAACAGATCTTGTCTTCATG
65 CAAAG-AAACAGATCTTGTCTCCCCA
* * * * * * * *
53392981 TACTGG-CGTGAAGTAGATCAAAGATACCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATC
1 TACTGGTGGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCACATACTGGTCGTGAAGTAGATC
*
53393045 AAAGAAACAGATCTTGTCTCCTCA
66 AAAGAAACAGATCTTGTCTCCCCA
* * * ** *
53393069 TACTGGTGGTGGAGTAGATCGAAGAAAACAGATCTTGTCTTTATGTACTGG-CATGAAGTAGATC
1 TACTGGTGGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCACATACTGGTCGTGAAGTAGATC
* * *
53393133 AAAGATACCAGATCTTGCCTTCCCA
66 AAAGA-AACAGATCTTGTCTCCCCA
* * * * *
53393158 TACTGGTGGCGAAGCAGATCAAAG-AAACAGATCTTGTCTCCCCATACTGGTAGT-AGAGTAGAT
1 TACTGGTGGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCACATACTGGTCGTGA-AGTAGAT
* * * ***
53393221 CGAAGAAAATAGATCTTGTCTTCATG
65 CAAAG-AAACAGATCTTGTCTCCCCA
* * ** * * * * * *
53393247 TATTGG-CGTGAAGTAGATCAAAGGTACCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATC
1 TACTGGTGGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCACATACTGGTCGTGAAGTAGATC
53393311 AAAGAAACAGATCTTGTCTCCCCA
66 AAAGAAACAGATCTTGTCTCCCCA
* * * * **
53393335 TACTGGTGGTGGAGTAGATCGAAGAAAATAGATCTTATCTTCATGTACTGG-CGTGAAGTAGATC
1 TACTGGTGGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCACATACTGGTCGTGAAGTAGATC
53393399 AAAGA
66 AAAGA
53393404 TAGCAGGTCC
Statistics
Matches: 329, Mismatches: 84, Indels: 21
0.76 0.19 0.05
Matches are distributed among these distances:
88 124 0.38
89 203 0.62
90 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (89 bp):
TACTGGTGGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCACATACTGGTCGTGAAGTAGATC
AAAGAAACAGATCTTGTCTCCCCA
Found at i:53393420 original size:44 final size:45
Alignment explanation
Indices: 53392876--53393503 Score: 463
Period size: 44 Copynumber: 14.2 Consensus size: 45
53392866 GAAAGAAAGT
** * *
53392876 AGATCTTGTCTTCATGTACTGGTGGCGAAGCAGATCAAAGA-AAC
1 AGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGATAAC
* * * * *
53392920 AGATCTTGTCTCCCCATACTGGTGGTGGAA-TAGGTCGAAGAAAAC
1 AGATCTTGTCTTCACATACTGGTGGT-GAAGTAGATCAAAGATAAC
** * *
53392965 AGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGATACC
1 AGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGATAAC
* * * *
53393009 AGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGA-AAC
1 AGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGATAAC
* * * * *
53393053 AGATCTTGTCTCCTCATACTGGTGGTGGAGTAGATCGAAGAAAAC
1 AGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGATAAC
* ** ** *
53393098 AGATCTTGTCTTTATGTACTGG-CATGAAGTAGATCAAAGATACC
1 AGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGATAAC
* * * *
53393142 AGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGA-AAC
1 AGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGATAAC
* * * * * *
53393186 AGATCTTGTCTCCCCATACTGGTAGT-AGAGTAGATCGAAGAAAAT
1 AGATCTTGTCTTCACATACTGGTGGTGA-AGTAGATCAAAGATAAC
** * * * *
53393231 AGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCAAAGGTACC
1 AGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGATAAC
* * * *
53393275 AGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGA-AAC
1 AGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGATAAC
* * * * * *
53393319 AGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCGAAGAAAAT
1 AGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGATAAC
* ** * *
53393364 AGATCTTATCTTCATGTACTGG-CGTGAAGTAGATCAAAGATAGC
1 AGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGATAAC
* * * * * * * *
53393408 AGGTCCTGTCTTC-CTATA-TCGGTAGCGAAGTGGATCGAATAT-AT
1 AGATCTTGTCTTCAC-ATACT-GGTGGTGAAGTAGATCAAAGATAAC
* * * * ** *
53393452 AGATTTTATCTTCCCATACTGGTGGCGAAGTAGATTGAAGATTAC
1 AGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGATAAC
53393497 AGATCTT
1 AGATCTT
53393504 ATCTCCCTAA
Statistics
Matches: 446, Mismatches: 121, Indels: 33
0.74 0.20 0.05
Matches are distributed among these distances:
43 5 0.01
44 292 0.65
45 149 0.33
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (45 bp):
AGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGATAAC
Found at i:53393679 original size:44 final size:45
Alignment explanation
Indices: 53393629--53393713 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 45
53393619 CGAGGAAAAC
** *
53393629 AGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGAAAGT
1 AGATCTTGTCTTCACATACTGGTCGTGAAGTAGATCGAAGAAAGT
* *
53393673 AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGA
1 AGATCTTGTCTTCACATACTGGTCGTGAAGTAGATCGAAGA
53393714 TGCAAGTCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
44 18 0.51
45 17 0.49
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.31
Consensus pattern (45 bp):
AGATCTTGTCTTCACATACTGGTCGTGAAGTAGATCGAAGAAAGT
Found at i:53395361 original size:21 final size:20
Alignment explanation
Indices: 53395307--53395362 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
53395297 ATATTTATCA
* *
53395307 TTATACCATTATTTATTATTG
1 TTATATCATTA-TTATTATGG
*
53395328 TTATATTATTTATTATTATGG
1 TTATATCA-TTATTATTATGG
53395349 TTATTATCATTATT
1 TTA-TATCATTATT
53395363 TCTATATTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 22 0.76
22 7 0.24
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (20 bp):
TTATATCATTATTATTATGG
Found at i:53401162 original size:5 final size:5
Alignment explanation
Indices: 53401154--53401179 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
53401144 GAGATGGAAT
53401154 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
53401180 ATATTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:53402112 original size:9 final size:9
Alignment explanation
Indices: 53402098--53402134 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
53402088 TATAGTTTGA
53402098 TATTCGAAT
1 TATTCGAAT
53402107 TATTCGAAT
1 TATTCGAAT
*
53402116 TATTCGAGT
1 TATTCGAAT
53402125 TATTCGAAT
1 TATTCGAAT
53402134 T
1 T
53402135 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:53402208 original size:9 final size:9
Alignment explanation
Indices: 53402189--53402230 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
53402179 TCGAGTTGAT
*
53402189 TCGAATAAC
1 TCGATTAAC
*
53402198 TCTATTAAC
1 TCGATTAAC
53402207 TCGATTAAC
1 TCGATTAAC
*
53402216 TCGAATAAC
1 TCGATTAAC
53402225 TCGATT
1 TCGATT
53402231 TGTTTAACTC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (9 bp):
TCGATTAAC
Found at i:53409481 original size:49 final size:49
Alignment explanation
Indices: 53409424--53409527 Score: 145
Period size: 49 Copynumber: 2.1 Consensus size: 49
53409414 TCATGTATTA
* * ** * *
53409424 TAATTTTATACAGTGTTGAGTTTTTTATTCATGATATTGAACTCAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTCAATTT
*
53409473 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTCAATTT
53409522 TAATTT
1 TAATTT
53409528 GTTTTTTTTC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.31, C:0.09, G:0.10, T:0.51
Consensus pattern (49 bp):
TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTCAATTT
Found at i:53411278 original size:39 final size:41
Alignment explanation
Indices: 53411233--53411338 Score: 135
Period size: 44 Copynumber: 2.5 Consensus size: 41
53411223 TTTCCTTATG
* *
53411233 CTATTACACCTCTATTCCATTCAACCAAACACAAGAA-TAC
1 CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
53411273 C-ATTACGCCTCTATTCCATTACATTCAACCAAACAAAAGAATTAC
1 CTATTACGCCTCTATT-C----CATTCAACCAAACAAAAGAATTAC
53411318 CTATTACGCCTCTATTCCATT
1 CTATTACGCCTCTATTCCATT
53411339 ACGCCTCTAT
Statistics
Matches: 57, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
39 13 0.23
40 2 0.04
41 4 0.07
44 19 0.33
45 5 0.09
46 14 0.25
ACGTcount: A:0.36, C:0.31, G:0.04, T:0.29
Consensus pattern (41 bp):
CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
Found at i:53411313 original size:44 final size:46
Alignment explanation
Indices: 53411250--53411340 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
53411240 ACCTCTATTC
*
53411250 CATTCAACCAAACACAAGAA-TACC-ATTACGCCTCTATTCCATTA
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
53411294 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
53411340 C
1 C
53411341 GCCTCTATTC
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 19 0.43
45 4 0.09
46 21 0.48
ACGTcount: A:0.38, C:0.31, G:0.04, T:0.26
Consensus pattern (46 bp):
CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
Found at i:53411341 original size:16 final size:16
Alignment explanation
Indices: 53411320--53411356 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
53411310 AGAATTACCT
53411320 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
53411336 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
53411352 ATTAC
1 ATTAC
53411357 AGCGAACCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.22, C:0.35, G:0.05, T:0.38
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:53412082 original size:29 final size:29
Alignment explanation
Indices: 53412026--53412082 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
53412016 TCAGTTTAAC
* * *
53412026 AAATTTTTTTATTTTTTTAGATTTTTATA
1 AAATTTTATTATTTATTTAGATTATTATA
53412055 AAATTTTAATTATTTATTTA-ATTATTAT
1 AAATTTT-ATTATTTATTTAGATTATTAT
53412083 TTGGCCATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 14 0.58
30 10 0.42
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (29 bp):
AAATTTTATTATTTATTTAGATTATTATA
Found at i:53413274 original size:11 final size:11
Alignment explanation
Indices: 53413230--53413276 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
53413220 TATTTAAAAA
*
53413230 TTTTATGAAGTT
1 TTTTAT-AATTT
53413242 TTTTATAATTT
1 TTTTATAATTT
*
53413253 TCTTT-TGATTT
1 T-TTTATAATTT
53413264 TTTTATAATTT
1 TTTTATAATTT
53413275 TT
1 TT
53413277 AAATTATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
10 3 0.10
11 18 0.60
12 9 0.30
ACGTcount: A:0.21, C:0.02, G:0.06, T:0.70
Consensus pattern (11 bp):
TTTTATAATTT
Found at i:53416159 original size:14 final size:14
Alignment explanation
Indices: 53416140--53416168 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
53416130 TCATCGTGCG
53416140 AAATCACATGGCCT
1 AAATCACATGGCCT
53416154 AAATCACATGGCCT
1 AAATCACATGGCCT
53416168 A
1 A
53416169 CCGCACAGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.28, G:0.14, T:0.21
Consensus pattern (14 bp):
AAATCACATGGCCT
Found at i:53417087 original size:19 final size:20
Alignment explanation
Indices: 53417051--53417099 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
53417041 ATTTTTCTTG
53417051 ATTTATATTATAAAATTATT
1 ATTTATATTATAAAATTATT
*
53417071 ATTTA-ATTA-AAATATTATA
1 ATTTATATTATAAA-ATTATT
*
53417090 AATTATATTA
1 ATTTATATTA
53417100 ATTAAAGTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 3 0.12
19 13 0.52
20 9 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTATATTATAAAATTATT
Found at i:53417105 original size:24 final size:27
Alignment explanation
Indices: 53417055--53417105 Score: 81
Period size: 24 Copynumber: 2.0 Consensus size: 27
53417045 TTCTTGATTT
53417055 ATATTATAAAATTATTATTTAATTAAA
1 ATATTATAAAATTATTATTTAATTAAA
53417082 ATATTAT-AAATTA-TA-TTAATTAAA
1 ATATTATAAAATTATTATTTAATTAAA
53417106 GTTAAGATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 9 0.38
25 2 0.08
26 6 0.25
27 7 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
ATATTATAAAATTATTATTTAATTAAA
Found at i:53417118 original size:30 final size:27
Alignment explanation
Indices: 53417055--53417119 Score: 76
Period size: 30 Copynumber: 2.3 Consensus size: 27
53417045 TTCTTGATTT
*
53417055 ATATTATAAAATTATTATTTAATTAAA
1 ATATTATAAAATTATTATTAAATTAAA
* *
53417082 ATATTATAAATTATATTAATTAAAGTTAAG
1 ATATTATAAAAT-TATT-ATTAAA-TTAAA
53417112 ATATTATA
1 ATATTATA
53417120 TTATAGGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 11 0.34
28 4 0.12
29 5 0.16
30 12 0.38
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (27 bp):
ATATTATAAAATTATTATTAAATTAAA
Found at i:53417261 original size:3 final size:3
Alignment explanation
Indices: 53417253--53417293 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
53417243 GTGAATTAAA
*
53417253 TAT TAT TA- TAT TAT TAT TAT ATAT TGT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TA
53417294 ACTAATACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:53421404 original size:30 final size:31
Alignment explanation
Indices: 53421370--53421430 Score: 115
Period size: 30 Copynumber: 2.0 Consensus size: 31
53421360 GAAAAAAACT
53421370 TAATAATTTAATGACTTAAATAA-AACTTTC
1 TAATAATTTAATGACTTAAATAATAACTTTC
53421400 TAATAATTTAATGACTTAAATAATAACTTTC
1 TAATAATTTAATGACTTAAATAATAACTTTC
53421431 GAATGATTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 23 0.77
31 7 0.23
ACGTcount: A:0.46, C:0.10, G:0.03, T:0.41
Consensus pattern (31 bp):
TAATAATTTAATGACTTAAATAATAACTTTC
Found at i:53425025 original size:20 final size:20
Alignment explanation
Indices: 53425000--53425043 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
53424990 AGTAAGTTTT
53425000 TTCTCTTTTGTTGCTTCTAG
1 TTCTCTTTTGTTGCTTCTAG
53425020 TTCTCTTTTGTTGCTTCTAG
1 TTCTCTTTTGTTGCTTCTAG
53425040 TTCT
1 TTCT
53425044 GTAATATAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.05, C:0.20, G:0.14, T:0.61
Consensus pattern (20 bp):
TTCTCTTTTGTTGCTTCTAG
Found at i:53425823 original size:60 final size:58
Alignment explanation
Indices: 53425746--53425873 Score: 166
Period size: 60 Copynumber: 2.2 Consensus size: 58
53425736 CCTTTCGCTG
* * * **
53425746 AAGTTTCAGTCTCAACAAAGATGGGCTGCTCAAGTTTCTTTGCTTTTTTTCAAACTTTTC
1 AAGTTTCAGTCTCAACAAAGATGGACGGCTCAAGTTTCATT--TTAATTTCAAACTTTTC
* * *
53425806 AAGTTTTAGTCTTAACAAAGATGGACGGCTCAAGTTTCATTTTAATTTCAAACTTTTT
1 AAGTTTCAGTCTCAACAAAGATGGACGGCTCAAGTTTCATTTTAATTTCAAACTTTTC
53425864 AAGTTTCAGT
1 AAGTTTCAGT
53425874 TTTGTTATTA
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
58 23 0.39
60 36 0.61
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.41
Consensus pattern (58 bp):
AAGTTTCAGTCTCAACAAAGATGGACGGCTCAAGTTTCATTTTAATTTCAAACTTTTC
Found at i:53431895 original size:69 final size:69
Alignment explanation
Indices: 53431815--53431949 Score: 243
Period size: 69 Copynumber: 2.0 Consensus size: 69
53431805 CTTCTTCGGC
* *
53431815 TGATGTTGACTTGGTGCAATCACCAGATGTTTCAAGTGGTAATGCTCGGTCTATCACAATAACAT
1 TGATGTTGACTTAGTGCAATCACCAGATGTTTCAAGTGGTAATGCTCGGTCTATCACAAGAACAT
53431880 CGAT
66 CGAT
*
53431884 TGATGTTGACTTAGTGCAATCACCAGATGTTTCAAGTGGTAATGCTCGGTCTATTACAAGAACAT
1 TGATGTTGACTTAGTGCAATCACCAGATGTTTCAAGTGGTAATGCTCGGTCTATCACAAGAACAT
53431949 C
66 C
53431950 TGAAGGTGTC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 63 1.00
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (69 bp):
TGATGTTGACTTAGTGCAATCACCAGATGTTTCAAGTGGTAATGCTCGGTCTATCACAAGAACAT
CGAT
Found at i:53434056 original size:20 final size:19
Alignment explanation
Indices: 53434031--53434068 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
53434021 AAATAATTTG
53434031 AATTTTAAAAATTAATTTTT
1 AATTTTAAAAATT-ATTTTT
*
53434051 AATTTTGAAAATTATTTT
1 AATTTTAAAAATTATTTT
53434069 AAGTTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (19 bp):
AATTTTAAAAATTATTTTT
Found at i:53436952 original size:50 final size:50
Alignment explanation
Indices: 53436877--53436973 Score: 169
Period size: 50 Copynumber: 1.9 Consensus size: 50
53436867 GGTAATACTG
53436877 ACATTTGAACTCAACAAAGATTCATTTCGTCAACAACCAAAATATCACCA
1 ACATTTGAACTCAACAAAGATTCATTTCGTCAACAACCAAAATATCACCA
*
53436927 ACATTTGAACTCAACAAA-AGTTCATTTCGTCTACAACCAAAATATCA
1 ACATTTGAACTCAACAAAGA-TTCATTTCGTCAACAACCAAAATATCA
53436974 TTGCCACAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
49 1 0.02
50 44 0.98
ACGTcount: A:0.43, C:0.25, G:0.06, T:0.26
Consensus pattern (50 bp):
ACATTTGAACTCAACAAAGATTCATTTCGTCAACAACCAAAATATCACCA
Found at i:53438515 original size:3 final size:3
Alignment explanation
Indices: 53438507--53438571 Score: 51
Period size: 3 Copynumber: 21.0 Consensus size: 3
53438497 GGGTTTTAAA
* * * * *
53438507 AAT AAT AAT ACT AAT AAT AAT GAG AAT AAT -AT GAAT GAT AAT AAA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
53438552 AAT AAT AAAT AAT GAAT AAT
1 AAT AAT -AAT AAT -AAT AAT
53438572 CTACGGTTTG
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
2 2 0.04
3 38 0.79
4 8 0.17
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:53440220 original size:44 final size:44
Alignment explanation
Indices: 53440119--53440808 Score: 434
Period size: 44 Copynumber: 15.4 Consensus size: 44
53440109 CTTTGATCCA
* * * ** **
53440119 CTCCACTGTAACTTCAGGGAGATAAAACTTGTAGCTTCCATCCA
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTTAATCTG
* * *
53440163 TTCCACT-CTAACTTCAGGGAGATAAGACTTATAGCTTTAATCTG
1 CTCCACTGC-AACTTCAGGGAGATAAGATTTGTAGCTTTAATCTG
* * * * *
53440207 CTCCGCTGCAACTTCAGGGGGATGAGATTTGT-GTTTTCTATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTT-AATCTG
* * * *
53440251 CTTCACTACGACCTT-AGGGAGATAA-AGTGTGTAGCTTTAATCTG
1 CTCCACTGC-AACTTCAGGGAGATAAGA-TTTGTAGCTTTAATCTG
** *** * ** *
53440295 CTCTGCTGCAACTTCAAAAAGTTAAGATTTGCTATTTTTAACCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGCTTTAATCTG
* * * * **
53440340 CTCCACTGTAATTTTAGGGAGATAAGGTTTGCGGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTTAATCTG
* * *
53440384 CTCCGCTGCAACTTTAAGGAGATAAGATTTGTAGCCTGTCTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTAG-C--T-TT-AATCTG
* ** *
53440433 CTCCACTGCAATTTCAGGGAGATAAGATTTGTTTATTTTTAACCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTG--TAGCTTTAATCTG
* * *
53440479 CTCCACTGCAACTTCAAGGAGATAAGGTTTATAGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTTAATCTG
* * ** ** *
53440523 CTCTACTGCAACTTCAGAGAGATAAGATTTGCTTTCTCCAATCTA
1 CTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGCTTTAATCTG
* * * ** *
53440568 TTCTACTGCAACTTCAGGGAGATAAGGTTTGTTTATTTTTAACCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTG--TAGCTTTAATCTG
* * * * * * *
53440614 CTCCACTACAACTTTAAGGAAATAAGGTTTATAGCTTTAATCTA
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTTAATCTG
* * ** * *** *
53440658 CTCTACTGCAACTTCAGAGAGATAATTTTTGCTATCTCCGATCTA
1 CTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGCTTTAATCTG
* * * * * *
53440703 CTCAACTGCAACTTCAGGGAGATAAGATCTATAACTTCAACCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTTAATCTG
* * * * *
53440747 CTCCACTACAACTTCAGGGAGACAATATTTGTAGCCTTTAGTTTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTAG-CTTTAATCTG
*
53440792 ATCCACTGCAACTTCAG
1 CTCCACTGCAACTTCAG
53440809 ACTCCACTGT
Statistics
Matches: 484, Mismatches: 142, Indels: 39
0.73 0.21 0.06
Matches are distributed among these distances:
43 9 0.02
44 238 0.49
45 133 0.27
46 63 0.13
47 3 0.01
48 3 0.01
49 33 0.07
51 2 0.00
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTTAATCTG
Found at i:53440410 original size:89 final size:88
Alignment explanation
Indices: 53440164--53440779 Score: 385
Period size: 89 Copynumber: 6.9 Consensus size: 88
53440154 TTCCATCCAT
* ** * * * *
53440164 TCCACT-CTAACTTCAGGGAGATAAGACTTATAGCTTTAATCTGCTCCGCTGCAACTTCAGGGGG
1 TCCACTGC-AACTTTAGGGAGATAAGGTTTGTAGCTTTAATCTGCTCCACTGCAACTTCAAGGAG
* *
53440228 ATGAGATTTGTGTTTTCT-ATCTGC
65 ATAAGATTTGTATTTT-TAATCTGC
* * * * * * ** ** *
53440252 TTCACTACGACCTTAGGGAGATAAAGTGTGTAGCTTTAATCTGCTCTGCTGCAACTTCAAAAAGT
1 TCCACTGCAACTTTAGGGAGATAAGGTTTGTAGCTTTAATCTGCTCCACTGCAACTTCAAGGAGA
*
53440317 TAAGATTTGCTATTTTTAACCTGC
66 TAAGATTTG-TATTTTTAATCTGC
* * ** * *
53440341 TCCACTGTAATTTTAGGGAGATAAGGTTTGCGGCTTTAATCTGCTCCGCTGCAACTTTAAGGAGA
1 TCCACTGCAACTTTAGGGAGATAAGGTTTGTAGCTTTAATCTGCTCCACTGCAACTTCAAGGAGA
*
53440406 TAAGATTTGTAGCCTGTCTTCAATCTGC
66 TAAGATTTGTA---T-T-TTTAATCTGC
* ** *
53440434 TCCACTGCAA-TTTCAGGGAGATAAGATTTGTTTATTTTTAACCTGCTCCACTGCAACTTCAAGG
1 TCCACTGCAACTTT-AGGGAGATAAGGTTTG--TAGCTTTAATCTGCTCCACTGCAACTTCAAGG
* * **
53440498 AGATAAGGTTTATAGCTTTAATCTGC
63 AGATAAGATTTGTATTTTTAATCTGC
* * * * ** ** ** * *
53440524 TCTACTGCAACTTCAGAGAGATAAGATTTGCTTTCTCCAATCTATTCTACTGCAACTTCAGGGAG
1 TCCACTGCAACTTTAGGGAGATAAGGTTTG-TAGCTTTAATCTGCTCCACTGCAACTTCAAGGAG
* *
53440589 ATAAGGTTTGTTTATTTTTAACCTGC
65 ATAAGATTTG--TATTTTTAATCTGC
* * * * * *
53440615 TCCACTACAACTTTAAGGAAATAAGGTTTATAGCTTTAATCTACTCTACTGCAACTTC-AGAGAG
1 TCCACTGCAACTTTAGGGAGATAAGGTTTGTAGCTTTAATCTGCTCCACTGCAACTTCAAG-GAG
** * *** *
53440679 ATAATTTTTGCTATCTCCGATCTAC
65 ATAAGATTTG-TATTTTTAATCTGC
* * * * * * * * * *
53440704 TCAACTGCAACTTCAGGGAGATAAGATCTATAACTTCAACCTGCTCCACTACAACTTCAGGGAGA
1 TCCACTGCAACTTTAGGGAGATAAGGTTTGTAGCTTTAATCTGCTCCACTGCAACTTCAAGGAGA
* *
53440769 CAATATTTGTA
66 TAAGATTTGTA
53440780 GCCTTTAGTT
Statistics
Matches: 407, Mismatches: 105, Indels: 32
0.75 0.19 0.06
Matches are distributed among these distances:
88 61 0.15
89 169 0.42
90 68 0.17
91 36 0.09
92 4 0.01
93 32 0.08
95 37 0.09
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (88 bp):
TCCACTGCAACTTTAGGGAGATAAGGTTTGTAGCTTTAATCTGCTCCACTGCAACTTCAAGGAGA
TAAGATTTGTATTTTTAATCTGC
Found at i:53440501 original size:139 final size:136
Alignment explanation
Indices: 53440317--53440730 Score: 539
Period size: 135 Copynumber: 3.0 Consensus size: 136
53440307 TTCAAAAAGT
* * * * ***
53440317 TAAGATTTG-CTATTTTTAACCTGCTCCACTGTAATTTTAGGGAGATAAGGTTTGCGGCTTTAAT
1 TAAGATTTGTTTATTTTTAACCTGCTCCACTGCAACTTTAAGGAGATAAGGTTTATAGCTTTAAT
** * * * * * *
53440381 CTGCTCCGCTGCAACTTTA-AGGAGATAAGATTTGTAGCCTGTCTTCAATCTGCTCCACTGCAAT
66 CTGCTCTACTGCAACTTCAGA-GAGATAAGATTT-T-G-CTATCTCCAATCTACTCAACTGCAAC
53440445 TTCAGGGAGA
127 TTCAGGGAGA
*
53440455 TAAGATTTGTTTATTTTTAACCTGCTCCACTGCAACTTCAAGGAGATAAGGTTTATAGCTTTAAT
1 TAAGATTTGTTTATTTTTAACCTGCTCCACTGCAACTTTAAGGAGATAAGGTTTATAGCTTTAAT
* * *
53440520 CTGCTCTACTGCAACTTCAGAGAGATAAGA-TTTGCTTTCTCCAATCTATTCTACTGCAACTTCA
66 CTGCTCTACTGCAACTTCAGAGAGATAAGATTTTGCTATCTCCAATCTACTCAACTGCAACTTCA
53440584 GGGAGA
131 GGGAGA
* * *
53440590 TAAGGTTTGTTTATTTTTAACCTGCTCCACTACAACTTTAAGGAAATAAGGTTTATAGCTTTAAT
1 TAAGATTTGTTTATTTTTAACCTGCTCCACTGCAACTTTAAGGAGATAAGGTTTATAGCTTTAAT
* * *
53440655 CTACTCTACTGCAACTTCAGAGAGATAA-TTTTTGCTATCTCCGATCTACTCAACTGCAACTTCA
66 CTGCTCTACTGCAACTTCAGAGAGATAAGATTTTGCTATCTCCAATCTACTCAACTGCAACTTCA
53440719 GGGAGA
131 GGGAGA
53440725 TAAGAT
1 TAAGAT
53440731 CTATAACTTC
Statistics
Matches: 245, Mismatches: 28, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
135 159 0.65
136 1 0.00
137 1 0.00
138 11 0.04
139 72 0.29
140 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (136 bp):
TAAGATTTGTTTATTTTTAACCTGCTCCACTGCAACTTTAAGGAGATAAGGTTTATAGCTTTAAT
CTGCTCTACTGCAACTTCAGAGAGATAAGATTTTGCTATCTCCAATCTACTCAACTGCAACTTCA
GGGAGA
Found at i:53440551 original size:90 final size:93
Alignment explanation
Indices: 53440337--53440597 Score: 262
Period size: 95 Copynumber: 2.8 Consensus size: 93
53440327 TATTTTTAAC
* * * * * ** * *
53440337 CTGCTCCACTGTAATTTTAGGGAGATAAGGTTTGC-GGCTTTAATCTGCTCCGCTGCAACTTTAA
1 CTGCTCCACTGCAACTTCAGAGAGATAAGATTTGCTTTCTTTAATCTGCTCCACTGCAACTTCAA
* *
53440401 GGAGATAAGATTTGTAGCCTGTCTTCAAT
66 GGAGATAAGGTTTATAGCC-GTCTTCAAT
* * * * *
53440430 CTGCTCCACTGCAATTTCAGGGAGATAAGATTTGTTTATTTTTAACCTGCTCCACTGCAACTTCA
1 CTGCTCCACTGCAACTTCAGAGAGATAAGATTTGCTT-TCTTTAATCTGCTCCACTGCAACTTCA
53440495 AGGAGATAAGGTTTATAG-C-T-TT-AAT
65 AGGAGATAAGGTTTATAGCCGTCTTCAAT
* ** ** * *
53440520 CTGCTCTACTGCAACTTCAGAGAGATAAGATTTGCTTTCTCCAATCTATTCTACTGCAACTTCAG
1 CTGCTCCACTGCAACTTCAGAGAGATAAGATTTGCTTTCTTTAATCTGCTCCACTGCAACTTCAA
53440585 GGAGATAAGGTTT
66 GGAGATAAGGTTT
53440598 GTTTATTTTT
Statistics
Matches: 142, Mismatches: 24, Indels: 8
0.82 0.14 0.05
Matches are distributed among these distances:
89 33 0.23
90 36 0.25
91 2 0.01
92 1 0.01
93 31 0.22
94 1 0.01
95 38 0.27
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (93 bp):
CTGCTCCACTGCAACTTCAGAGAGATAAGATTTGCTTTCTTTAATCTGCTCCACTGCAACTTCAA
GGAGATAAGGTTTATAGCCGTCTTCAAT
Found at i:53440626 original size:135 final size:135
Alignment explanation
Indices: 53440327--53440809 Score: 513
Period size: 135 Copynumber: 3.6 Consensus size: 135
53440317 TAAGATTTGC
** * * * *** *
53440327 TATTTTTAACCTGCTCCACTGTAATTTTAGGGAGATAAGGTTTGCGGCTTTAATCTGCTCCGCTG
1 TATTTTTAACCTGCTCCACTACAACTTCAAGGAGATAAGGTTTATAGCTTTAATCTGCTCCACTG
* * * * * *
53440392 CAACTTTA-AGGAGATAAGATTTGTAGCCTGTCTTCAATCTGCTCCACTGCAATTTCAGGGAGAT
66 CAACTTCAGA-GAGATAAGA-TT-T-G-CTATCTCCAATCTACTCAACTGCAACTTCAGGGAGAT
*
53440456 AAGATTTGTT
126 AAGGTTTGTT
* *
53440466 TATTTTTAACCTGCTCCACTGCAACTTCAAGGAGATAAGGTTTATAGCTTTAATCTGCTCTACTG
1 TATTTTTAACCTGCTCCACTACAACTTCAAGGAGATAAGGTTTATAGCTTTAATCTGCTCCACTG
* * *
53440531 CAACTTCAGAGAGATAAGATTTGCTTTCTCCAATCTATTCTACTGCAACTTCAGGGAGATAAGGT
66 CAACTTCAGAGAGATAAGATTTGCTATCTCCAATCTACTCAACTGCAACTTCAGGGAGATAAGGT
53440596 TTGTT
131 TTGTT
* * * *
53440601 TATTTTTAACCTGCTCCACTACAACTTTAAGGAAATAAGGTTTATAGCTTTAATCTACTCTACTG
1 TATTTTTAACCTGCTCCACTACAACTTCAAGGAGATAAGGTTTATAGCTTTAATCTGCTCCACTG
** *
53440666 CAACTTCAGAGAGATAATTTTTGCTATCTCCGATCTACTCAACTGCAACTTCAGGGAGATAA-G-
66 CAACTTCAGAGAGATAAGATTTGCTATCTCCAATCTACTCAACTGCAACTTCAGGGAGATAAGGT
* * *
53440729 ATCTA
131 TTGTT
** * * * ** * * * *
53440734 TAACTTCAACCTGCTCCACTACAACTTCAGGGAGACAATATTTGTAGCCTTTAGTTTGATCCACT
1 TATTTTTAACCTGCTCCACTACAACTTCAAGGAGATAAGGTTTATAG-CTTTAATCTGCTCCACT
53440799 GCAACTTCAGA
65 GCAACTTCAGA
53440810 CTCCACTGTA
Statistics
Matches: 297, Mismatches: 45, Indels: 9
0.85 0.13 0.03
Matches are distributed among these distances:
133 39 0.13
134 24 0.08
135 157 0.53
136 1 0.00
137 1 0.00
138 2 0.01
139 72 0.24
140 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (135 bp):
TATTTTTAACCTGCTCCACTACAACTTCAAGGAGATAAGGTTTATAGCTTTAATCTGCTCCACTG
CAACTTCAGAGAGATAAGATTTGCTATCTCCAATCTACTCAACTGCAACTTCAGGGAGATAAGGT
TTGTT
Done.