Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 166 of 187
Found at i:48982365 original size:25 final size:25
Alignment explanation
Indices: 48982330--48982389 Score: 111
Period size: 25 Copynumber: 2.4 Consensus size: 25
48982320 GTTCATTTAT
48982330 TTAAGTAAGTTTAATGTTTGTTATGA
1 TTAA-TAAGTTTAATGTTTGTTATGA
48982356 TTAATAAGTTTAATGTTTGTTATGA
1 TTAATAAGTTTAATGTTTGTTATGA
48982381 TTAATAAGT
1 TTAATAAGT
48982390 GTTTTCATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 30 0.88
26 4 0.12
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (25 bp):
TTAATAAGTTTAATGTTTGTTATGA
Found at i:48989426 original size:15 final size:16
Alignment explanation
Indices: 48989403--48989432 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
48989393 TTTTTCACAC
48989403 TCATCTTCTTTTTCTT
1 TCATCTTCTTTTTCTT
48989419 TCAT-TTCTTTTTCT
1 TCATCTTCTTTTTCT
48989433 CTCACTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.07, C:0.23, G:0.00, T:0.70
Consensus pattern (16 bp):
TCATCTTCTTTTTCTT
Found at i:48989426 original size:33 final size:34
Alignment explanation
Indices: 48989349--48989438 Score: 91
Period size: 36 Copynumber: 2.6 Consensus size: 34
48989339 TTTTGCGCTC
48989349 TCATTTCTTTCTTCAATCTCACTCTCTTTTTCAGTTT
1 TCATTTCTTT-TTCAATCTCACTCTCTTTTTCA--TT
*
48989386 TCTTTTCTTTTTCACA-CTCA-TCTTCTTTTTC-TT
1 TCATTTCTTTTTCA-ATCTCACTC-TCTTTTTCATT
48989419 TCATTTCTTTTTC--TCTCACT
1 TCATTTCTTTTTCAATCTCACT
48989439 TTTTCGATTT
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
31 4 0.09
32 1 0.02
33 14 0.30
35 2 0.04
36 16 0.34
37 10 0.21
ACGTcount: A:0.11, C:0.28, G:0.01, T:0.60
Consensus pattern (34 bp):
TCATTTCTTTTTCAATCTCACTCTCTTTTTCATT
Found at i:48991313 original size:13 final size:13
Alignment explanation
Indices: 48991292--48991345 Score: 63
Period size: 13 Copynumber: 4.1 Consensus size: 13
48991282 TAAATGTTCC
*
48991292 AATTCAGCTGATT
1 AATTAAGCTGATT
*
48991305 AATTAAGCTGTTT
1 AATTAAGCTGATT
* *
48991318 ACTTAGAACTGATT
1 AATTA-AGCTGATT
48991332 AATTAAGCTGATT
1 AATTAAGCTGATT
48991345 A
1 A
48991346 CTTAGACCTG
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
13 23 0.70
14 10 0.30
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (13 bp):
AATTAAGCTGATT
Found at i:48991329 original size:27 final size:27
Alignment explanation
Indices: 48991299--48991356 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
48991289 TCCAATTCAG
*
48991299 CTGATTAATTAAGCTGTTTACTTAGAA
1 CTGATTAATTAAGCTGATTACTTAGAA
*
48991326 CTGATTAATTAAGCTGATTACTTAGAC
1 CTGATTAATTAAGCTGATTACTTAGAA
48991353 CTGA
1 CTGA
48991357 AGAGTTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.38
Consensus pattern (27 bp):
CTGATTAATTAAGCTGATTACTTAGAA
Found at i:48992873 original size:26 final size:26
Alignment explanation
Indices: 48992844--48992910 Score: 89
Period size: 26 Copynumber: 2.6 Consensus size: 26
48992834 TACATGGTTA
48992844 CTCACACGAGCTGTGAAATAAGAATG
1 CTCACACGAGCTGTGAAATAAGAATG
* ** **
48992870 CTCACACGAGCAGTGAAATTGGTCTG
1 CTCACACGAGCTGTGAAATAAGAATG
48992896 CTCACACGAGCTGTG
1 CTCACACGAGCTGTG
48992911 GGTCGGAATG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.30, C:0.24, G:0.25, T:0.21
Consensus pattern (26 bp):
CTCACACGAGCTGTGAAATAAGAATG
Found at i:48995286 original size:14 final size:15
Alignment explanation
Indices: 48995269--48995299 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
48995259 TTCAGTCTTA
48995269 TTTTTATT-GTTGTT
1 TTTTTATTAGTTGTT
48995283 TTTTTATTAGTTGTT
1 TTTTTATTAGTTGTT
48995298 TT
1 TT
48995300 ATTTGTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.10, C:0.00, G:0.13, T:0.77
Consensus pattern (15 bp):
TTTTTATTAGTTGTT
Found at i:49001696 original size:22 final size:22
Alignment explanation
Indices: 49001634--49001705 Score: 117
Period size: 22 Copynumber: 3.3 Consensus size: 22
49001624 GGATGTCAAA
* **
49001634 CATGAGAGCTTAGTACGTGAAA
1 CATGAGAGCTTAGTACGTTAGC
49001656 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
49001678 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
49001700 CATGAG
1 CATGAG
49001706 GGTTTGGGTA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:49004641 original size:24 final size:25
Alignment explanation
Indices: 49004612--49004680 Score: 74
Period size: 24 Copynumber: 2.8 Consensus size: 25
49004602 CAAATAATAA
49004612 AATAATAATACAGCATAACTTTTA-
1 AATAATAATACAGCATAACTTTTAG
* *
49004636 AGTAATAATAC-GTAATAA-TTTTAG
1 AATAATAATACAG-CATAACTTTTAG
49004660 AATAATAATACA-CGATAACTT
1 AATAATAATACAGC-ATAACTT
49004681 AAAAAATATG
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
23 6 0.17
24 28 0.78
25 2 0.06
ACGTcount: A:0.49, C:0.10, G:0.07, T:0.33
Consensus pattern (25 bp):
AATAATAATACAGCATAACTTTTAG
Found at i:49006443 original size:44 final size:44
Alignment explanation
Indices: 49006353--49006690 Score: 473
Period size: 44 Copynumber: 7.7 Consensus size: 44
49006343 GTAATTTTCA
* * *
49006353 ACCTACTCCACAGCTGGTCA-GG-GCTAGGACTTACAATCTTCT
1 ACCTATTCCACTGCTGGTCAGGGAGCTAGGACTTACAATCTTCC
*
49006395 ACCTATTCCACTGCTGGTCAGGGAGCTAGGACTTACAGTCTTCC
1 ACCTATTCCACTGCTGGTCAGGGAGCTAGGACTTACAATCTTCC
*
49006439 ACCTATTCCACTGCTGGTCAGGGAGCTAGGACTTACAATCTTCT
1 ACCTATTCCACTGCTGGTCAGGGAGCTAGGACTTACAATCTTCC
* *
49006483 ACCAATTCCACTGCTGGTCAGGGAGCTAGGACTTACAGTCTTCC
1 ACCTATTCCACTGCTGGTCAGGGAGCTAGGACTTACAATCTTCC
* * * * *
49006527 ACCTATTCCAATGTTGTTCAGGGAGCTAGGATTTACAATCTTTC
1 ACCTATTCCACTGCTGGTCAGGGAGCTAGGACTTACAATCTTCC
* * * * *
49006571 GCCTATTCCACTGCTGTTCAGGGATCTAGGACTTTCAGTCTTCC
1 ACCTATTCCACTGCTGGTCAGGGAGCTAGGACTTACAATCTTCC
*
49006615 ACCTATTCCACTGCTGGTCAGGGAGCTAGGACTTACAATCTTCT
1 ACCTATTCCACTGCTGGTCAGGGAGCTAGGACTTACAATCTTCC
* * *
49006659 ACCTATTCCACTACTGTTCAGGGAGATAGGAC
1 ACCTATTCCACTGCTGGTCAGGGAGCTAGGAC
49006691 ATATAGTTTC
Statistics
Matches: 261, Mismatches: 33, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
42 18 0.07
43 2 0.01
44 241 0.92
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (44 bp):
ACCTATTCCACTGCTGGTCAGGGAGCTAGGACTTACAATCTTCC
Found at i:49007978 original size:15 final size:16
Alignment explanation
Indices: 49007943--49007986 Score: 63
Period size: 15 Copynumber: 2.7 Consensus size: 16
49007933 CCTTTGCGGG
49007943 TTTTTTACTTTTTCATCA
1 TTTTTTA-TTTTT-ATCA
49007961 TTTTTTATTTTT-TCA
1 TTTTTTATTTTTATCA
49007976 TTTTTTATTTT
1 TTTTTTATTTT
49007987 GACTTTGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 14 0.54
17 5 0.19
18 7 0.27
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTTATTTTTATCA
Found at i:49008010 original size:30 final size:30
Alignment explanation
Indices: 49007969--49008026 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
49007959 CATTTTTTAT
*
49007969 TTTTTCATTTTTTATTTTGACTTTGATTAA
1 TTTTTCATTTTTGATTTTGACTTTGATTAA
* *
49007999 TTTTTCTTTTTTGCTTTTGACTTTGATT
1 TTTTTCATTTTTGATTTTGACTTTGATT
49008027 TTTCTCCTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.14, C:0.09, G:0.09, T:0.69
Consensus pattern (30 bp):
TTTTTCATTTTTGATTTTGACTTTGATTAA
Found at i:49008040 original size:30 final size:29
Alignment explanation
Indices: 49007970--49008039 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
49007960 ATTTTTTATT
* *
49007970 TTTTCATTTTTT-ATTTTGACTTTGATTAA
1 TTTTCCTTTTTTGCTTTTGACTTTGATT-A
*
49007999 TTTTTCTTTTTTGCTTTTGACTTTGATT-
1 TTTTCCTTTTTTGCTTTTGACTTTGATTA
49008027 TTTCTCCTTTTTT
1 TTT-TCCTTTTTT
49008040 TTAATTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
28 3 0.09
29 18 0.51
30 14 0.40
ACGTcount: A:0.11, C:0.11, G:0.07, T:0.70
Consensus pattern (29 bp):
TTTTCCTTTTTTGCTTTTGACTTTGATTA
Found at i:49012511 original size:24 final size:25
Alignment explanation
Indices: 49012470--49012538 Score: 79
Period size: 24 Copynumber: 2.8 Consensus size: 25
49012460 CAAATAATAA
* **
49012470 AATAATAATAAAGCATAACTTTTA-
1 AATAATAATACATAATAACTTTTAG
*
49012494 AGTAATAATACATAATAA-TTTTAG
1 AATAATAATACATAATAACTTTTAG
*
49012518 AATAATAATACATGATAACTT
1 AATAATAATACATAATAACTT
49012539 CAAAAATATG
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
23 5 0.14
24 30 0.81
25 2 0.05
ACGTcount: A:0.52, C:0.07, G:0.06, T:0.35
Consensus pattern (25 bp):
AATAATAATACATAATAACTTTTAG
Found at i:49028630 original size:17 final size:16
Alignment explanation
Indices: 49028608--49028642 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
49028598 ACCACCAAAT
*
49028608 TGACACTTGAAGATCAG
1 TGACACTAGAAGAT-AG
49028625 TGACACTAGAAGATAG
1 TGACACTAGAAGATAG
49028641 TG
1 TG
49028643 GCTTGATACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (16 bp):
TGACACTAGAAGATAG
Found at i:49036788 original size:20 final size:20
Alignment explanation
Indices: 49036754--49036795 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
49036744 AACTATTTAA
** *
49036754 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
49036774 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
49036794 AT
1 AT
49036796 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:49047208 original size:114 final size:114
Alignment explanation
Indices: 49047061--49047812 Score: 745
Period size: 114 Copynumber: 6.8 Consensus size: 114
49047051 AAAATAAGCA
* * * *
49047061 TTAGCGGCATTTTTGAGAAAGCGCTACAAAAAAACCTAAGCCCAACGACGCTGTTTCCTGAGCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
*
49047126 TCGGGGATTTAGCGGCGTTTCTAAGAAAGCGCCGCTAATGCTCAGGGCT
66 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
*
49047175 TTAGCGGCGTTTTT-AGAAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
1 TTAGCGGCGTTTTTGAG-AAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
*
49047239 TTCGGGGATTTAGCGGCGTTTATAAGAAAGCGCCGCTAATGCTCAGGGCT
65 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
* * * *
49047289 TTAGCGGCGTTTTTGGGAAAGCGCCACAAAAAAACCTAAGCCCCACGATGTCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* *
49047354 TCGGGGATTTAGCGGCATTTTTAAGAAAGCGCAGCTAATGCTCAGGGCT
66 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
* *
49047403 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTTTGAGCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* * * * * * * *
49047468 TCAGGTATTTAGTGGCGTTTTTAAGATTAGCGACG-T--T-TTTA--G-A
66 TCGGGGATTTAGCGGCGTTTTTAAGA-AAGCGCCGCTAATGCTCAGGGCT
** * ** * * * **** * * *** * *
49047511 AAAGCGCCG----CAAAAAAAC-CTA-AGCCCAA-CGACGCCGTTTTCTGA-G-C--TTTCGGGG
1 TTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAAACCTAAGCC--CAAC-GACGCCGTTTTCTGAG
* * *
49047565 ATTTAGCGGCG-TTTA-T---------AAGAAAGCGCCGCTAATGCTCAGGGCT
63 CTTT--CGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
* * * *
49047608 TTAGCGGCGTTTTTGGGAAAGCGCCACAAAAAAACCTAAGCCCCACGATGTCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
*
49047673 TCGGGGATTTAGCGGCATTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
66 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
* *
49047722 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTTTGAGCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* *
49047787 TCAGGGATTTAGTGGCGTTTTTAAGA
66 TCGGGGATTTAGCGGCGTTTTTAAGA
49047813 TTAGCGGCGT
Statistics
Matches: 509, Mismatches: 92, Indels: 74
0.75 0.14 0.11
Matches are distributed among these distances:
90 6 0.01
91 5 0.01
93 1 0.00
94 2 0.00
96 1 0.00
97 6 0.01
100 9 0.02
101 15 0.03
102 10 0.02
103 11 0.02
104 16 0.03
105 9 0.02
108 6 0.01
109 1 0.00
111 2 0.00
112 1 0.00
113 2 0.00
114 400 0.79
115 6 0.01
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (114 bp):
TTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
Found at i:49047558 original size:91 final size:91
Alignment explanation
Indices: 49047403--49047584 Score: 294
Period size: 91 Copynumber: 2.0 Consensus size: 91
49047393 GCTCAGGGCT
* *
49047403 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTTTGAGCTT
1 TTAGCGACGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* * *
49047468 TCAGGTATTTAGTGGCGTTTTTAAGA
66 TCAGGGATTTAGCGGCGTTTATAAGA
49047494 TTAGCGACGTTTTT-AGAAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
1 TTAGCGACGTTTTTGAG-AAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
*
49047558 TTCGGGGATTTAGCGGCGTTTATAAGA
65 TTCAGGGATTTAGCGGCGTTTATAAGA
49047585 AAGCGCCGCT
Statistics
Matches: 84, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
90 2 0.02
91 82 0.98
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.27
Consensus pattern (91 bp):
TTAGCGACGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
TCAGGGATTTAGCGGCGTTTATAAGA
Found at i:49047648 original size:205 final size:205
Alignment explanation
Indices: 49047289--49047698 Score: 640
Period size: 205 Copynumber: 2.0 Consensus size: 205
49047279 GCTCAGGGCT
* * * * * *
49047289 TTAGCGGCGTTTTTGGGAAAGCGCCACAAAAAAACCTAAGCCCCACGATGTCGTTTTCTGAGCTT
1 TTAGCGACGTTTTTAGAAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
*
49047354 TCGGGGATTTAGCGGCATTTTTAAGAAAGCGCAGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGA
66 TCGGGGATTTAGCGGCATTTATAAGAAAGCGCAGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGA
* * * *
49047419 GAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTTTGAGCTTTCAGGTATTTAGTGGC
131 GAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCAGGGATTTAGCGGC
*
49047484 GTTTTTAAGA
196 ATTTTTAAGA
*
49047494 TTAGCGACGTTTTTAGAAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
1 TTAGCGACGTTTTTAGAAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* * *
49047559 TCGGGGATTTAGCGGCGTTTATAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGG
66 TCGGGGATTTAGCGGCATTTATAAGAAAGCGCAGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGA
* * * *
49047624 GAAAGCGCCACAAAAAAACCTAAGCCCCACGATGTCGTTTTCTGAGCTTTCGGGGATTTAGCGGC
131 GAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCAGGGATTTAGCGGC
49047689 ATTTTTAAGA
196 ATTTTTAAGA
49047699 AAGCGCCGCT
Statistics
Matches: 185, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
205 185 1.00
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.27
Consensus pattern (205 bp):
TTAGCGACGTTTTTAGAAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
TCGGGGATTTAGCGGCATTTATAAGAAAGCGCAGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGA
GAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCAGGGATTTAGCGGC
ATTTTTAAGA
Found at i:49047761 original size:319 final size:319
Alignment explanation
Indices: 49047175--49047884 Score: 1366
Period size: 319 Copynumber: 2.2 Consensus size: 319
49047165 GCTCAGGGCT
49047175 TTAGCGGCGTTTTTAGAAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTAGAAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
49047240 TCGGGGATTTAGCGGCGTTTATAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGG
66 TCGGGGATTTAGCGGCGTTTATAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGG
49047305 GAAAGCGCCACAAAAAAACCTAAGCCCCACGATGTCGTTTTCTGAGCTTTCGGGGATTTAGCGGC
131 GAAAGCGCCACAAAAAAACCTAAGCCCCACGATGTCGTTTTCTGAGCTTTCGGGGATTTAGCGGC
49047370 ATTTTTAAGAAAGCGCAGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAA
196 ATTTTTAAGAAAGCGCAGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAA
*
49047435 AACCTAAGCCCAACGACGCCGTTTTTTGAGCTTTCAGGTATTTAGTGGCGTTTTTAAGA
261 AACCTAAGCCCAACGACGCCGTTTTTTGAGCTTTCAGGGATTTAGTGGCGTTTTTAAGA
*
49047494 TTAGCGACGTTTTTAGAAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTAGAAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
49047559 TCGGGGATTTAGCGGCGTTTATAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGG
66 TCGGGGATTTAGCGGCGTTTATAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGG
49047624 GAAAGCGCCACAAAAAAACCTAAGCCCCACGATGTCGTTTTCTGAGCTTTCGGGGATTTAGCGGC
131 GAAAGCGCCACAAAAAAACCTAAGCCCCACGATGTCGTTTTCTGAGCTTTCGGGGATTTAGCGGC
*
49047689 ATTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAA
196 ATTTTTAAGAAAGCGCAGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAA
49047754 AACCTAAGCCCAACGACGCCGTTTTTTGAGCTTTCAGGGATTTAGTGGCGTTTTTAAGA
261 AACCTAAGCCCAACGACGCCGTTTTTTGAGCTTTCAGGGATTTAGTGGCGTTTTTAAGA
* * *
49047813 TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCTGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTAGAAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
49047878 TCGGGGA
66 TCGGGGA
49047885 NNNNNNNNNN
Statistics
Matches: 384, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
319 384 1.00
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (319 bp):
TTAGCGGCGTTTTTAGAAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
TCGGGGATTTAGCGGCGTTTATAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGG
GAAAGCGCCACAAAAAAACCTAAGCCCCACGATGTCGTTTTCTGAGCTTTCGGGGATTTAGCGGC
ATTTTTAAGAAAGCGCAGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAA
AACCTAAGCCCAACGACGCCGTTTTTTGAGCTTTCAGGGATTTAGTGGCGTTTTTAAGA
Found at i:49048248 original size:15 final size:15
Alignment explanation
Indices: 49048228--49048258 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
49048218 CATATTTTAT
49048228 GGTTTAGGGAGTATG
1 GGTTTAGGGAGTATG
*
49048243 GGTTTAGGGATTATG
1 GGTTTAGGGAGTATG
49048258 G
1 G
49048259 ATTAGTGGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.45, T:0.35
Consensus pattern (15 bp):
GGTTTAGGGAGTATG
Found at i:49048526 original size:15 final size:15
Alignment explanation
Indices: 49048506--49048551 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
49048496 TATTTTAAGG
*
49048506 TTTAGAGAGTATGGA
1 TTTAGAGATTATGGA
49048521 TTTAGAGATTAT-GA
1 TTTAGAGATTATGGA
* *
49048535 ATTAGGGATTATGGA
1 TTTAGAGATTATGGA
49048550 TT
1 TT
49048552 ATGGTTTAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.33, C:0.00, G:0.28, T:0.39
Consensus pattern (15 bp):
TTTAGAGATTATGGA
Found at i:49048588 original size:7 final size:7
Alignment explanation
Indices: 49048578--49048616 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
49048568 AATTTAAGGT
49048578 TTAGGGG
1 TTAGGGG
49048585 TTAGGGG
1 TTAGGGG
49048592 TTTAGGGG
1 -TTAGGGG
**
49048600 TTAGATG
1 TTAGGGG
49048607 TTAGGGG
1 TTAGGGG
49048614 TTA
1 TTA
49048617 AGATCAGTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 20 0.74
8 7 0.26
ACGTcount: A:0.18, C:0.00, G:0.46, T:0.36
Consensus pattern (7 bp):
TTAGGGG
Found at i:49048595 original size:15 final size:15
Alignment explanation
Indices: 49048574--49048616 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
49048564 TTGGAATTTA
49048574 AGGTTTAGGGGTTAG
1 AGGTTTAGGGGTTAG
*
49048589 GGGTTTAGGGGTTAG
1 AGGTTTAGGGGTTAG
*
49048604 ATG-TTAGGGGTTA
1 AGGTTTAGGGGTTA
49048617 AGATCAGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.19, C:0.00, G:0.47, T:0.35
Consensus pattern (15 bp):
AGGTTTAGGGGTTAG
Found at i:49049468 original size:49 final size:48
Alignment explanation
Indices: 49049415--49049563 Score: 121
Period size: 49 Copynumber: 3.2 Consensus size: 48
49049405 AAATTTATAA
49049415 AAAATAAAATAAAAAATTTTTAGCATAGAAAAACGGTGTCATTTTGTTC
1 AAAATAAAATAAAAAATTTTTAGCATAGAAAAAC-GTGTCATTTTGTTC
* ***** * * * **
49049464 AAAATGAAATAGCGGCGTTTTT----TATAAAAAC--GTCAATTTATAA
1 AAAATAAAATA-AAAAATTTTTAGCATAGAAAAACGTGTCATTTTGTTC
*
49049507 AAAATAAAATAAAAAATTTTTAGCATAGCAAAACGATGTCATTTTGTTC
1 AAAATAAAATAAAAAATTTTTAGCATAGAAAAACG-TGTCATTTTGTTC
49049556 AAAATAAA
1 AAAATAAA
49049564 TCAATTTATA
Statistics
Matches: 69, Mismatches: 23, Indels: 16
0.64 0.21 0.15
Matches are distributed among these distances:
42 5 0.07
43 18 0.26
46 15 0.22
49 26 0.38
50 5 0.07
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.32
Consensus pattern (48 bp):
AAAATAAAATAAAAAATTTTTAGCATAGAAAAACGTGTCATTTTGTTC
Found at i:49049573 original size:68 final size:68
Alignment explanation
Indices: 49049496--49049628 Score: 205
Period size: 68 Copynumber: 2.0 Consensus size: 68
49049486 TATAAAAACG
* * *
49049496 TCAATTTATAAAAAATAAAATAAAAAATTTTTAGC-ATAGCAAAACGATGTCATTTTGTTCAAAA
1 TCAATTTATAAAAAACAAAATAAAAAATTTTTA-CAAAAGCAAAACGACGTCATTTTGTTCAAAA
49049560 TAAA
65 TAAA
* *
49049564 TCAATTTATAAAAAACAAAATAAAAAATTTTTACAAAAGCAAAACGGCGTCGTTTTGTTCAAAAT
1 TCAATTTATAAAAAACAAAATAAAAAATTTTTACAAAAGCAAAACGACGTCATTTTGTTCAAAAT
49049629 GAAAAAAATT
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
67 1 0.02
68 58 0.98
ACGTcount: A:0.50, C:0.11, G:0.08, T:0.31
Consensus pattern (68 bp):
TCAATTTATAAAAAACAAAATAAAAAATTTTTACAAAAGCAAAACGACGTCATTTTGTTCAAAAT
AAA
Found at i:49049601 original size:23 final size:25
Alignment explanation
Indices: 49049555--49049607 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
49049545 TCATTTTGTT
*
49049555 CAAAATAAATCAATTTATAAAAAA-
1 CAAAATAAATAAATTTATAAAAAAG
* *
49049579 CAAAATAAA-AAATTTTTACAAAAG
1 CAAAATAAATAAATTTATAAAAAAG
49049603 CAAAA
1 CAAAA
49049608 CGGCGTCGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.66, C:0.09, G:0.02, T:0.23
Consensus pattern (25 bp):
CAAAATAAATAAATTTATAAAAAAG
Found at i:49049818 original size:106 final size:107
Alignment explanation
Indices: 49049691--49049885 Score: 313
Period size: 106 Copynumber: 1.8 Consensus size: 107
49049681 GCGGCGTTTT
* *
49049691 AAAACGCCGCAAAAAATAAATCAATTTATAAAAAATAAAATAAGAAA-TTTTTAGCATAACAAAA
1 AAAACGCCGCAAAAAATAAATCAATTTATAAAAAACAAAATAA-AAATTTTTTAGAATAACAAAA
*
49049755 CGGTGTCATTTTGTTCAAAATGAAATAGCGGCATTTTTTTATA
65 CGGCGTCATTTTGTTCAAAATGAAATAGCGGCATTTTTTTATA
*
49049798 AAAACGCCGC-AAAAATAAATCAATTTATAAAAAACAAAATAAAAATTTTTTAGAATAGCAAAAC
1 AAAACGCCGCAAAAAATAAATCAATTTATAAAAAACAAAATAAAAATTTTTTAGAATAACAAAAC
**
49049862 GGCGTGTTTTTGTTCAAAATGAAA
66 GGCGTCATTTTGTTCAAAATGAAA
49049886 AAAAATTTGC
Statistics
Matches: 81, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
105 3 0.04
106 68 0.84
107 10 0.12
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.28
Consensus pattern (107 bp):
AAAACGCCGCAAAAAATAAATCAATTTATAAAAAACAAAATAAAAATTTTTTAGAATAACAAAAC
GGCGTCATTTTGTTCAAAATGAAATAGCGGCATTTTTTTATA
Found at i:49049990 original size:26 final size:26
Alignment explanation
Indices: 49049959--49050008 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
49049949 AAAACGCCGC
49049959 AAAAATAAATCAATTTATAAAAAACA
1 AAAAATAAATCAATTTATAAAAAACA
49049985 AAAAATAAATCAATTTATAAAAAA
1 AAAAATAAATCAATTTATAAAAAA
49050009 GCAATAATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (26 bp):
AAAAATAAATCAATTTATAAAAAACA
Found at i:49052857 original size:23 final size:23
Alignment explanation
Indices: 49052827--49053274 Score: 338
Period size: 23 Copynumber: 19.7 Consensus size: 23
49052817 GAAATTTGAT
49052827 AGTGCTGCAAATTGAAGTGTTTA
1 AGTGCTGCAAATTGAAGTGTTTA
*
49052850 AGTGCTGCAAATTGAAGTATTT-
1 AGTGCTGCAAATTGAAGTGTTTA
* *
49052872 AGTTGCTGGAAATTG-AGATGTTTT
1 AG-TGCTGCAAATTGAAG-TGTTTA
* *
49052896 A-TCGCTGC-AATTGAGGTGTATA
1 AGT-GCTGCAAATTGAAGTGTTTA
* * **
49052918 AATGTTGTTAATTGATA-TGTTTA
1 AGTGCTGCAAATTGA-AGTGTTTA
*
49052941 AGTGCTGCAAATTTAAGTGTTTA
1 AGTGCTGCAAATTGAAGTGTTTA
* *
49052964 AATGCTGTAAATTGAAGTGTTTA
1 AGTGCTGCAAATTGAAGTGTTTA
49052987 AGTGCTGCAAATTGAAGTGTTT-
1 AGTGCTGCAAATTGAAGTGTTTA
* *
49053009 AGTTGCTGGAAATTG-AGATATGTT-
1 AG-TGCTGCAAATTGAAG-TGT-TTA
* * * *
49053033 ATTGCTG-TAATTGAGGTGTGTA
1 AGTGCTGCAAATTGAAGTGTTTA
* * **
49053055 AATGTTGTTAATTGATA-TG-TTA
1 AGTGCTGCAAATTGA-AGTGTTTA
*
49053077 AGTGCTGCAAATTTAAGTGTTTA
1 AGTGCTGCAAATTGAAGTGTTTA
* *
49053100 AATGCTGTAAATTGAAGTGTTTA
1 AGTGCTGCAAATTGAAGTGTTTA
*
49053123 AGTGCTGCAAATTGAAGTATTT-
1 AGTGCTGCAAATTGAAGTGTTTA
* *
49053145 AGTTGCTGGAAATTG-AGATGTTTT
1 AG-TGCTGCAAATTGAAG-TGTTTA
* *
49053169 A-TCGCTG-TAATT-AAGGTGTATA
1 AGT-GCTGCAAATTGAA-GTGTTTA
* * **
49053191 AATGTTGTTAATTGATA-TGTTTA
1 AGTGCTGCAAATTGA-AGTGTTTA
49053214 AGTGCTGCAAATTGAAGTGTTTA
1 AGTGCTGCAAATTGAAGTGTTTA
49053237 AGTGCTGCAAATTGAAGTGTTT-
1 AGTGCTGCAAATTGAAGTGTTTA
49053259 AGTTGCTGCAAATTGA
1 AG-TGCTGCAAATTGA
49053275 GATGTGTTAT
Statistics
Matches: 341, Mismatches: 54, Indels: 60
0.75 0.12 0.13
Matches are distributed among these distances:
21 2 0.01
22 70 0.21
23 262 0.77
24 6 0.02
25 1 0.00
ACGTcount: A:0.30, C:0.06, G:0.24, T:0.40
Consensus pattern (23 bp):
AGTGCTGCAAATTGAAGTGTTTA
Found at i:49052903 original size:46 final size:46
Alignment explanation
Indices: 49052829--49053274 Score: 396
Period size: 46 Copynumber: 9.8 Consensus size: 46
49052819 AATTTGATAG
* * **
49052829 TGCTGCAAATTGA-AGTGTTTAAGTGCTGCAAATTGAAGTATTTAGT
1 TGCTGTAAATTGAGA-TGTTTAAGTGCTGCAAATTGAAGTGTTTAAA
* * * *
49052875 TGCTGGAAATTGAGATGTTTTA-TCGCTGC-AATTGAGGTGTATAAA
1 TGCTGTAAATTGAGATGTTTAAGT-GCTGCAAATTGAAGTGTTTAAA
* * * *
49052920 TGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTAAGTGTTTAAA
1 TGCTGTAAATTGAGATGTTTAAGTGCTGCAAATTGAAGTGTTTAAA
**
49052966 TGCTGTAAATTGA-AGTGTTTAAGTGCTGCAAATTGAAGTGTTTAGT
1 TGCTGTAAATTGAGA-TGTTTAAGTGCTGCAAATTGAAGTGTTTAAA
* * * * * *
49053012 TGCTGGAAATTGAGATATGTT-ATTGCTG-TAATTGAGGTGTGTAAA
1 TGCTGTAAATTGAGATGT-TTAAGTGCTGCAAATTGAAGTGTTTAAA
* * * *
49053057 TGTTGTTAATTGATATG-TTAAGTGCTGCAAATTTAAGTGTTTAAA
1 TGCTGTAAATTGAGATGTTTAAGTGCTGCAAATTGAAGTGTTTAAA
* **
49053102 TGCTGTAAATTGA-AGTGTTTAAGTGCTGCAAATTGAAGTATTTAGT
1 TGCTGTAAATTGAGA-TGTTTAAGTGCTGCAAATTGAAGTGTTTAAA
* * * *
49053148 TGCTGGAAATTGAGATGTTTTA-TCGCTG-TAATT-AAGGTGTATAAA
1 TGCTGTAAATTGAGATGTTTAAGT-GCTGCAAATTGAA-GTGTTTAAA
* * * *
49053193 TGTTGTTAATTGATATGTTTAAGTGCTGCAAATTGAAGTGTTTAAG
1 TGCTGTAAATTGAGATGTTTAAGTGCTGCAAATTGAAGTGTTTAAA
*
49053239 TGCTGCAAATTGA-AGTGTTT-AGTTGCTGCAAATTGA
1 TGCTGTAAATTGAGA-TGTTTAAG-TGCTGCAAATTGA
49053275 GATGTGTTAT
Statistics
Matches: 319, Mismatches: 62, Indels: 38
0.76 0.15 0.09
Matches are distributed among these distances:
43 2 0.01
44 9 0.03
45 119 0.37
46 182 0.57
47 7 0.02
ACGTcount: A:0.30, C:0.07, G:0.24, T:0.40
Consensus pattern (46 bp):
TGCTGTAAATTGAGATGTTTAAGTGCTGCAAATTGAAGTGTTTAAA
Found at i:49053075 original size:137 final size:137
Alignment explanation
Indices: 49052829--49053274 Score: 770
Period size: 137 Copynumber: 3.3 Consensus size: 137
49052819 AATTTGATAG
49052829 TGCTGCAAATTGAAGTGTTTAAGTGCTGCAAATTGAAGTATTTAGTTGCTGGAAATTGAGATGTT
1 TGCTGCAAATTGAAGTGTTTAAGTGCTGCAAATTGAAGTATTTAGTTGCTGGAAATTGAGATGTT
*
49052894 TTATCGCTGCAATTGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTAAGT
66 TTATCGCTGTAATTGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTAAGT
49052959 GTTTAAA
131 GTTTAAA
* * * *
49052966 TGCTGTAAATTGAAGTGTTTAAGTGCTGCAAATTGAAGTGTTTAGTTGCTGGAAATTGAGATATG
1 TGCTGCAAATTGAAGTGTTTAAGTGCTGCAAATTGAAGTATTTAGTTGCTGGAAATTGAGATGTT
* *
49053031 TTATTGCTGTAATTGAGGTGTGTAAATGTTGTTAATTGATATG-TTAAGTGCTGCAAATTTAAGT
66 TTATCGCTGTAATTGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTAAGT
49053095 GTTTAAA
131 GTTTAAA
*
49053102 TGCTGTAAATTGAAGTGTTTAAGTGCTGCAAATTGAAGTATTTAGTTGCTGGAAATTGAGATGTT
1 TGCTGCAAATTGAAGTGTTTAAGTGCTGCAAATTGAAGTATTTAGTTGCTGGAAATTGAGATGTT
* *
49053167 TTATCGCTGTAATTAAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTGAAGT
66 TTATCGCTGTAATTGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTAAGT
*
49053232 GTTTAAG
131 GTTTAAA
49053239 TGCTGCAAATTGAAGTGTTT-AGTTGCTGCAAATTGA
1 TGCTGCAAATTGAAGTGTTTAAG-TGCTGCAAATTGA
49053275 GATGTGTTAT
Statistics
Matches: 291, Mismatches: 16, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
136 132 0.45
137 159 0.55
ACGTcount: A:0.30, C:0.07, G:0.24, T:0.40
Consensus pattern (137 bp):
TGCTGCAAATTGAAGTGTTTAAGTGCTGCAAATTGAAGTATTTAGTTGCTGGAAATTGAGATGTT
TTATCGCTGTAATTGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTAAGT
GTTTAAA
Found at i:49053304 original size:21 final size:22
Alignment explanation
Indices: 49053218--49053304 Score: 79
Period size: 23 Copynumber: 3.8 Consensus size: 22
49053208 TGTTTAAGTG
*
49053218 CTGCAAATTGAAGTGTTTAAGT-G
1 CTGCAAATTGAAGTG-TT-AGTCA
**
49053241 CTGCAAATTGAAGTGTTTAGTTG
1 CTGCAAATTGAAGTG-TTAGTCA
49053264 CTGCAAATTGAGATGTGTTA-TCA
1 CTGCAAATTGA-A-GTGTTAGTCA
*
49053287 CTGTAAATTGAAGTGTTA
1 CTGCAAATTGAAGTGTTA
49053305 AAGTGCTACT
Statistics
Matches: 58, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
21 6 0.10
22 4 0.07
23 41 0.71
24 4 0.07
25 3 0.05
ACGTcount: A:0.30, C:0.09, G:0.24, T:0.37
Consensus pattern (22 bp):
CTGCAAATTGAAGTGTTAGTCA
Found at i:49054282 original size:43 final size:43
Alignment explanation
Indices: 49054214--49054463 Score: 324
Period size: 43 Copynumber: 5.8 Consensus size: 43
49054204 TTTTCGTGAC
* * * *
49054214 CTTTAGTGGCGTTT-TTGGAGAAAGCGTCGCTAAAGGTCTTGTT
1 CTTTAGCGGCGTTTGTGGGA-AAAGCGCCGCTAAAGGTCTTGGT
* * **
49054257 TTTTAGCGGCGCTTCAGGGAAAAGCGCCGCTAAAGGTCTTGGT
1 CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGT
* *
49054300 CTTTAGCGGCGTTTGTGGGAAAAGCGCTGCTAAAGGTCCTGGT
1 CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGT
* * * *
49054343 CTTTAGCGGCATTTGTAGGAAAAGCACCGCTAAAGGTCCTGGT
1 CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGT
49054386 CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGT-TCTGGT
1 CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCT-TGGT
* *
49054429 CTTTAGCGGCGTTTGTGGGAAGAGCGACGCTAAAG
1 CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAG
49054464 TTAGCGGCAC
Statistics
Matches: 182, Mismatches: 23, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
43 179 0.98
44 3 0.02
ACGTcount: A:0.21, C:0.18, G:0.33, T:0.28
Consensus pattern (43 bp):
CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGT
Found at i:49056858 original size:20 final size:20
Alignment explanation
Indices: 49056835--49056943 Score: 76
Period size: 20 Copynumber: 5.5 Consensus size: 20
49056825 TTGCACAATT
*
49056835 GTGCCCCTGTTCACACTTCG
1 GTGCCCCTGTTCGCACTTCG
* *
49056855 GTGCCCCTATAT-ACACTTCG
1 GTGCCCCTGT-TCGCACTTCG
* * * * * *
49056875 GTGTCTCTATTTGCACGTCT
1 GTGCCCCTGTTCGCACTTCG
* * * *
49056895 ATGCTCCTGTTTGCACTTCA
1 GTGCCCCTGTTCGCACTTCG
*
49056915 GTGCCCCTGTTCGCACTTTG
1 GTGCCCCTGTTCGCACTTCG
49056935 GTGCCCCTG
1 GTGCCCCTG
49056944 ACTGCACGTA
Statistics
Matches: 69, Mismatches: 18, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
19 1 0.01
20 67 0.97
21 1 0.01
ACGTcount: A:0.11, C:0.34, G:0.20, T:0.35
Consensus pattern (20 bp):
GTGCCCCTGTTCGCACTTCG
Found at i:49079799 original size:29 final size:28
Alignment explanation
Indices: 49079751--49079810 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
49079741 AATGGCCAAC
*
49079751 CATGCTGCTGTTATGTTTTTATTGAAGTG
1 CATGCTGCTGTTATGATTTTATTG-AGTG
*
49079780 CATGCTGCT-TTGATGATTTTGTTGAGTG
1 CATGCTGCTGTT-ATGATTTTATTGAGTG
49079808 CAT
1 CAT
49079811 ACAGCCGGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.17, C:0.12, G:0.25, T:0.47
Consensus pattern (28 bp):
CATGCTGCTGTTATGATTTTATTGAGTG
Found at i:49080522 original size:57 final size:57
Alignment explanation
Indices: 49080459--49080574 Score: 214
Period size: 57 Copynumber: 2.0 Consensus size: 57
49080449 GCACTTCAAC
49080459 CAAAAATACCACAGCAGCATGGTTGGCCAATTTTCAATAGATTGCTTCCTTGCTGCA
1 CAAAAATACCACAGCAGCATGGTTGGCCAATTTTCAATAGATTGCTTCCTTGCTGCA
* *
49080516 CAAAAATATCACAGCAGCATGGTTGGCCAATTTTCAATAGATTGCTTCCTTGTTGCA
1 CAAAAATACCACAGCAGCATGGTTGGCCAATTTTCAATAGATTGCTTCCTTGCTGCA
49080573 CA
1 CA
49080575 TTTGTGAGCA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.29
Consensus pattern (57 bp):
CAAAAATACCACAGCAGCATGGTTGGCCAATTTTCAATAGATTGCTTCCTTGCTGCA
Found at i:49105372 original size:32 final size:32
Alignment explanation
Indices: 49105327--49105403 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
49105317 TAATAATTTT
* * * *
49105327 TAGAATATAATTAATATAAATCCTTGAAGAAAA
1 TAGAAT-TGATTAATACAAACCCTTAAAGAAAA
* *
49105360 TAGGATTGATTAATACAAACCCTTAAAGAAAT
1 TAGAATTGATTAATACAAACCCTTAAAGAAAA
49105392 TAGAATTGATTA
1 TAGAATTGATTA
49105404 GAAATTTGAC
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
32 32 0.86
33 5 0.14
ACGTcount: A:0.49, C:0.08, G:0.12, T:0.31
Consensus pattern (32 bp):
TAGAATTGATTAATACAAACCCTTAAAGAAAA
Found at i:49106174 original size:233 final size:238
Alignment explanation
Indices: 49105817--49106253 Score: 596
Period size: 233 Copynumber: 1.8 Consensus size: 238
49105807 GGCGTTTTGT
* * *
49105817 TTAAAGCGCCGCAAAATATCTTTACTAAAACGCGTAGTTTTAATTTTGATGTATACTAATATTAG
1 TTAAAACGCCGCAAAATATCTTAACTAAAACGCATAGTTTTAATTTT-ATGTATA-TAATATTAG
* * * * *
49105882 TGACGCTTACAAGAAAACGCCGTTAAAGATTATCTTTAGCGGTGATTTAGACGAAGCGCCACAAC
64 TGACGCTTACAAGAAAACGCCGTTAAAGAATAGCATTAGCGGCGATTTAGACGAAGCGCCACAAA
* * * * * * *
49105947 TTATCTTAAGAAAACGCAGTGTTTGGTCTTAAGCCATGTTACATTTAGTGGCGCTTATGGGAAAA
129 GTACCTTAACAAAACGCAGTGTTTCGTCTGAAGCCATGTTACATTTAGTGGCGCTTATAGCAAAA
49106012 CGCCGCAAAAAATCTCGATGTATACTTCAATTAGTGGCGCTGACG
194 CGCCGCAAAAAATCTCGATGTATACTTCAATTAGTGGCGCTGACG
*
49106057 TTAAAACGCCGCAAAATATCTTAACTAAAATGCATAGTTTTAA-TTT-TG-AT-T-ATATTAGTG
1 TTAAAACGCCGCAAAATATCTTAACTAAAACGCATAGTTTTAATTTTATGTATATAATATTAGTG
* * * * * * *
49106117 GCGTTTACTAGAAAACGCCGTTATAGAATAGCATTAGCGGCGCTTTAGCCGAAGCGCCGCAAAGT
66 ACGCTTACAAGAAAACGCCGTTAAAGAATAGCATTAGCGGCGATTTAGACGAAGCGCCACAAAGT
**
49106182 ACCTTAACAAAACGCAGTGTTTCGTCTGAAGTTATGTTACATTTAGTGGCGCTTATAGCAAAACG
131 ACCTTAACAAAACGCAGTGTTTCGTCTGAAGCCATGTTACATTTAGTGGCGCTTATAGCAAAACG
49106247 CCGCAAA
196 CCGCAAA
49106254 CTATCTGAAC
Statistics
Matches: 172, Mismatches: 25, Indels: 7
0.84 0.12 0.03
Matches are distributed among these distances:
233 125 0.73
234 1 0.01
236 2 0.01
237 2 0.01
239 3 0.02
240 39 0.23
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (238 bp):
TTAAAACGCCGCAAAATATCTTAACTAAAACGCATAGTTTTAATTTTATGTATATAATATTAGTG
ACGCTTACAAGAAAACGCCGTTAAAGAATAGCATTAGCGGCGATTTAGACGAAGCGCCACAAAGT
ACCTTAACAAAACGCAGTGTTTCGTCTGAAGCCATGTTACATTTAGTGGCGCTTATAGCAAAACG
CCGCAAAAAATCTCGATGTATACTTCAATTAGTGGCGCTGACG
Found at i:49106345 original size:189 final size:189
Alignment explanation
Indices: 49106110--49106502 Score: 603
Period size: 189 Copynumber: 2.1 Consensus size: 189
49106100 TTTTGATTAT
* * *
49106110 ATTAGTGGCGTTTACTAGAAAACGCCGTTATAGAATAGCATTAGCGGCGCTTTAGCCGAAGCGCC
1 ATTAGTGGCGCTTACTAGAAAACGCCGTTAAAGAATAGCATTAGCGGCGCTTTAGCCAAAGCGCC
*
49106175 GCAAAGTACCTTAACAAAACGCAGT-GTTTCGTCTGAAGTTATGTTACATTTAGTGGCGCTTATA
66 GCAAAGTACCTTAACAAAACGCAGTGGTTT-GTCTGAAGCTATGTTACATTTAGTGGCGCTTATA
*
49106239 -GCAAAACGCCGCAAACTATCTGAACCAAAACGCACCATTTTGGTCTCGATGTATACTTCA
130 TG-AAAACGCCGCAAAATATCTGAACCAAAACGCACCATTTTGGTCTCGATGTATACTTCA
* * * **
49106299 ATTAGTGGCGCTTACTAGAAAACGCCGTTAAAGAATA-TATTTAGCGGTGCTTTGGGTAAAGCGC
1 ATTAGTGGCGCTTACTAGAAAACGCCGTTAAAGAATAGCA-TTAGCGGCGCTTTAGCCAAAGCGC
* * *
49106363 CGCAACGTATCTTAACAAAACGCAGTGGTTTGTCTTAAGCTATGTTACATTTAGTGGCGCTTATA
65 CGCAAAGTACCTTAACAAAACGCAGTGGTTTGTCTGAAGCTATGTTACATTTAGTGGCGCTTATA
* *
49106428 TGAAAACGCCGCAAAATATCTGAACCAAAACGCACCGTTTTGGTCTCGATGTATACTTTA
130 TGAAAACGCCGCAAAATATCTGAACCAAAACGCACCATTTTGGTCTCGATGTATACTTCA
49106488 ATTAGTGGCGCTTAC
1 ATTAGTGGCGCTTAC
49106503 GTTCAAACGC
Statistics
Matches: 186, Mismatches: 15, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
188 1 0.01
189 180 0.97
190 5 0.03
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (189 bp):
ATTAGTGGCGCTTACTAGAAAACGCCGTTAAAGAATAGCATTAGCGGCGCTTTAGCCAAAGCGCC
GCAAAGTACCTTAACAAAACGCAGTGGTTTGTCTGAAGCTATGTTACATTTAGTGGCGCTTATAT
GAAAACGCCGCAAAATATCTGAACCAAAACGCACCATTTTGGTCTCGATGTATACTTCA
Found at i:49107119 original size:21 final size:21
Alignment explanation
Indices: 49107101--49107155 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
49107091 TAAGGTTTGT
49107101 AGTTTAGGGTTTAAAGTTTAA
1 AGTTTAGGGTTTAAAGTTTAA
* *
49107122 AGGTTACGGGTTTAAAGTATAA
1 AGTTTA-GGGTTTAAAGTTTAA
*
49107144 AGGTTACGGGTT
1 AGTTTA-GGGTT
49107156 AAACTTAGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 5 0.16
22 26 0.84
ACGTcount: A:0.31, C:0.04, G:0.29, T:0.36
Consensus pattern (21 bp):
AGTTTAGGGTTTAAAGTTTAA
Found at i:49107132 original size:22 final size:22
Alignment explanation
Indices: 49107107--49107155 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
49107097 TTGTAGTTTA
*
49107107 GGGTTTAAAGTTTAAAGGTTAC
1 GGGTTTAAAGTATAAAGGTTAC
49107129 GGGTTTAAAGTATAAAGGTTAC
1 GGGTTTAAAGTATAAAGGTTAC
49107151 GGGTT
1 GGGTT
49107156 AAACTTAGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.35
Consensus pattern (22 bp):
GGGTTTAAAGTATAAAGGTTAC
Found at i:49107741 original size:24 final size:25
Alignment explanation
Indices: 49107695--49107749 Score: 78
Period size: 24 Copynumber: 2.2 Consensus size: 25
49107685 TTCATTCCCT
*
49107695 AATTTCCCATTTCATATTCCCCCCC
1 AATTCCCCATTTCATATTCCCCCCC
49107720 AATTCCCCGATTTCAT-TT-CCCCCC
1 AATTCCCC-ATTTCATATTCCCCCCC
49107744 AATTCC
1 AATTCC
49107750 TATTCCCCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 12 0.43
25 9 0.32
26 7 0.25
ACGTcount: A:0.20, C:0.44, G:0.02, T:0.35
Consensus pattern (25 bp):
AATTCCCCATTTCATATTCCCCCCC
Found at i:49109163 original size:15 final size:15
Alignment explanation
Indices: 49109139--49109171 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
49109129 AAGGTTTCTA
*
49109139 TATTAGTATTAAATT
1 TATTACTATTAAATT
49109154 TATTACTATTAAATT
1 TATTACTATTAAATT
49109169 TAT
1 TAT
49109172 AAAAAATTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (15 bp):
TATTACTATTAAATT
Found at i:49109239 original size:24 final size:24
Alignment explanation
Indices: 49109211--49109292 Score: 71
Period size: 24 Copynumber: 3.2 Consensus size: 24
49109201 ATATTAGTAT
49109211 TATAAATATTGTTTTAATATAACC
1 TATAAATATTGTTTTAATATAACC
*
49109235 TATAAA-ATTTAAAAGTTTTCTAA-ATAA-T
1 TATAAATA-TT----G-TTT-TAATATAACC
49109263 TATAAATATTGTTTTAATATAACC
1 TATAAATATTGTTTTAATATAACC
49109287 TATAAA
1 TATAAA
49109293 ATTTAAAAGT
Statistics
Matches: 46, Mismatches: 2, Indels: 20
0.68 0.03 0.29
Matches are distributed among these distances:
22 3 0.07
23 8 0.17
24 15 0.33
28 9 0.20
29 8 0.17
30 3 0.07
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (24 bp):
TATAAATATTGTTTTAATATAACC
Found at i:49109265 original size:52 final size:52
Alignment explanation
Indices: 49109209--49109334 Score: 252
Period size: 52 Copynumber: 2.4 Consensus size: 52
49109199 CTATATTAGT
49109209 ATTATAAATATTGTTTTAATATAACCTATAAAATTTAAAAGTTTTCTAAATA
1 ATTATAAATATTGTTTTAATATAACCTATAAAATTTAAAAGTTTTCTAAATA
49109261 ATTATAAATATTGTTTTAATATAACCTATAAAATTTAAAAGTTTTCTAAATA
1 ATTATAAATATTGTTTTAATATAACCTATAAAATTTAAAAGTTTTCTAAATA
49109313 ATTATAAATATTGTTTTAATAT
1 ATTATAAATATTGTTTTAATAT
49109335 CTATATAAGT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (52 bp):
ATTATAAATATTGTTTTAATATAACCTATAAAATTTAAAAGTTTTCTAAATA
Found at i:49109320 original size:21 final size:21
Alignment explanation
Indices: 49109292--49109353 Score: 51
Period size: 21 Copynumber: 3.0 Consensus size: 21
49109282 TAACCTATAA
49109292 AATT-TAAAAGTTTTCTAAAT
1 AATTATAAAAGTTTTCTAAAT
*
49109312 AATTATAAATA-TTGTT-TTAAT
1 AATTATAAA-AGTT-TTCTAAAT
*
49109333 -ATCTATATAAGTTTTCTAAAT
1 AAT-TATAAAAGTTTTCTAAAT
49109354 TTATAAGGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 11
0.70 0.06 0.23
Matches are distributed among these distances:
20 9 0.27
21 21 0.64
22 3 0.09
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.48
Consensus pattern (21 bp):
AATTATAAAAGTTTTCTAAAT
Found at i:49109392 original size:15 final size:15
Alignment explanation
Indices: 49109368--49109400 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
49109358 AAGGTTTCTA
*
49109368 TATTAGTATTAAATT
1 TATTACTATTAAATT
49109383 TATTACTATTAAATT
1 TATTACTATTAAATT
49109398 TAT
1 TAT
49109401 AAATAATTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (15 bp):
TATTACTATTAAATT
Found at i:49109543 original size:229 final size:227
Alignment explanation
Indices: 49109077--49109496 Score: 716
Period size: 229 Copynumber: 1.8 Consensus size: 227
49109067 GATAACATTT
49109077 CTAAATAATTATAAATATTGTTTTAATATCTATATAAGTTTTCTAAACTTATAAGGTTTCTATAT
1 CTAAATAATTATAAATATTGTTTTAATATCTATATAAGTTTTCTAAACTTATAAGGTTTCTATAT
49109142 TAGTATTAAATTTATTACTATTAAATTTATAAAAAATTCTAAATATTGTTTTAATATCTATATTA
66 TAGTATTAAATTTATTACTATTAAATTTATAAAAAATTCTAAATATTGTTTTAATATCTATATTA
* ** * *
49109207 GTATTATAAATATTGTTTTAATATAACCTATAAAATTTAAAAGTTTTCTAAATAATTATAAATAT
131 GTATTATAAATATTGTTTTAATATAACCTATAAAATTTAAAAGTTTTCTAAAAAAAAAAAAATAA
*** *
49109272 TGTTTTAATATAACCTATAAAATTTAAAAGTTTT
196 TAACTTAATATAACC-ATAAAATTTAAAAG-TTA
*
49109306 CTAAATAATTATAAATATTGTTTTAATATCTATATAAGTTTTCTAAATTTATAAGGTTTCTATAT
1 CTAAATAATTATAAATATTGTTTTAATATCTATATAAGTTTTCTAAACTTATAAGGTTTCTATAT
*
49109371 TAGTATTAAATTTATTACTATTAAATTTATAAATAATTCTAAATATTGTTTTAATATCTATATTA
66 TAGTATTAAATTTATTACTATTAAATTTATAAAAAATTCTAAATATTGTTTTAATATCTATATTA
49109436 GTATTATAAATATTGTTTT-ATATAACCTATAAAATTTAAAAGTTTTCTAAAAAAAAAAAAA
131 GTATTATAAATATTGTTTTAATATAACCTATAAAATTTAAAAGTTTTCTAAAAAAAAAAAAA
49109497 CTTACATAAC
Statistics
Matches: 185, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
228 38 0.21
229 147 0.79
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (227 bp):
CTAAATAATTATAAATATTGTTTTAATATCTATATAAGTTTTCTAAACTTATAAGGTTTCTATAT
TAGTATTAAATTTATTACTATTAAATTTATAAAAAATTCTAAATATTGTTTTAATATCTATATTA
GTATTATAAATATTGTTTTAATATAACCTATAAAATTTAAAAGTTTTCTAAAAAAAAAAAAATAA
TAACTTAATATAACCATAAAATTTAAAAGTTA
Found at i:49109585 original size:25 final size:25
Alignment explanation
Indices: 49109551--49109604 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
49109541 AATACACACT
* * *
49109551 TACATAAATTAAATAAGTTACATAA
1 TACACAAATTAAACAACTTACATAA
*
49109576 TACACAAATTACACAACTTACATAA
1 TACACAAATTAAACAACTTACATAA
49109601 TACA
1 TACA
49109605 TAATTTACAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.54, C:0.17, G:0.02, T:0.28
Consensus pattern (25 bp):
TACACAAATTAAACAACTTACATAA
Found at i:49109606 original size:7 final size:8
Alignment explanation
Indices: 49109550--49109820 Score: 101
Period size: 9 Copynumber: 32.1 Consensus size: 8
49109540 TAATACACAC
49109550 TTACATAAA
1 TTACAT-AA
*
49109559 TTAAATAA
1 TTACATAA
49109567 GTTACATAA
1 -TTACATAA
*
49109576 -TACACAAA
1 TTACA-TAA
*
49109584 TTACACAA
1 TTACATAA
49109592 CTTACATAA
1 -TTACATAA
49109601 -TACATAA
1 TTACATAA
49109608 TTTACATAA
1 -TTACATAA
*
49109617 -TACACAA
1 TTACATAA
*
49109624 CTGACATAAA
1 -TTACAT-AA
49109634 CTTACATAA
1 -TTACATAA
*
49109643 -TACATATT
1 TTACATA-A
*
49109651 TTACATCAC
1 TTACAT-AA
49109660 TTACATAA
1 TTACATAA
*
49109668 -GACATAA
1 TTACATAA
49109675 CTTACATAA
1 -TTACATAA
*
49109684 GTTTCATAA
1 -TTACATAA
*
49109693 -TACACAA
1 TTACATAA
*
49109700 CTAACATAA
1 -TTACATAA
49109709 CTTACATAA
1 -TTACATAA
*
49109718 -TACACAA
1 TTACATAA
49109725 CTTACATAA
1 -TTACATAA
**
49109734 CCATCATAA
1 TTA-CATAA
*
49109743 -TACACAA
1 TTACATAA
49109750 CTTACATAA
1 -TTACATAA
*
49109759 GTTTCATAA
1 -TTACATAA
*
49109768 -TACACAA
1 TTACATAA
*
49109775 CTTACATAGC
1 -TTACATA-A
49109785 TTACATAA
1 TTACATAA
*
49109793 CTTACACAA
1 -TTACATAA
49109802 CTTACATAA
1 -TTACATAA
49109811 CTTACATAA
1 -TTACATAA
49109820 T
1 T
49109821 AAATAAGTTA
Statistics
Matches: 200, Mismatches: 37, Indels: 51
0.69 0.13 0.18
Matches are distributed among these distances:
7 49 0.25
8 10 0.05
9 132 0.66
10 9 0.05
ACGTcount: A:0.47, C:0.21, G:0.02, T:0.30
Consensus pattern (8 bp):
TTACATAA
Found at i:49109612 original size:25 final size:25
Alignment explanation
Indices: 49109563--49109616 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
49109553 CATAAATTAA
* *
49109563 ATAAGTTACATAATACACAAATTAC
1 ATAACTTACATAATACACAACTTAC
* * *
49109588 ACAACTTACATAATACATAATTTAC
1 ATAACTTACATAATACACAACTTAC
49109613 ATAA
1 ATAA
49109617 TACACAACTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.52, C:0.17, G:0.02, T:0.30
Consensus pattern (25 bp):
ATAACTTACATAATACACAACTTAC
Found at i:49109630 original size:25 final size:25
Alignment explanation
Indices: 49109601--49109821 Score: 264
Period size: 25 Copynumber: 8.7 Consensus size: 25
49109591 ACTTACATAA
*
49109601 TACATAATTTACATAATACACAACT
1 TACATAACTTACATAATACACAACT
* * **
49109626 GACATAAACTTACATAATACATATTT
1 TACAT-AACTTACATAATACACAACT
* * *
49109652 TACATCACTTACATAAGACATAACT
1 TACATAACTTACATAATACACAACT
* *
49109677 TACATAAGTTTCATAATACACAACT
1 TACATAACTTACATAATACACAACT
*
49109702 AACATAACTTACATAATACACAACT
1 TACATAACTTACATAATACACAACT
*
49109727 TACATAAC-CATCATAATACACAACT
1 TACATAACTTA-CATAATACACAACT
* *
49109752 TACATAAGTTTCATAATACACAACT
1 TACATAACTTACATAATACACAACT
*
49109777 TACATAGCTTACATAACTTACACAACT
1 TACATAACTTACATAA--TACACAACT
49109804 TACATAACTTACATAATA
1 TACATAACTTACATAATA
49109822 AATAAGTTAT
Statistics
Matches: 164, Mismatches: 27, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
24 1 0.01
25 119 0.73
26 20 0.12
27 24 0.15
ACGTcount: A:0.46, C:0.22, G:0.02, T:0.30
Consensus pattern (25 bp):
TACATAACTTACATAATACACAACT
Found at i:49109794 original size:18 final size:18
Alignment explanation
Indices: 49109548--49109819 Score: 168
Period size: 16 Copynumber: 16.1 Consensus size: 18
49109538 AATAATACAC
* *
49109548 ACTTACATAAATTAAATA
1 ACTTACATAACTTACATA
* *
49109566 AGTTACATAA--TACACA
1 ACTTACATAACTTACATA
* *
49109582 AATTACACAACTTACATA
1 ACTTACATAACTTACATA
*
49109600 A--TACATAATTTACATA
1 ACTTACATAACTTACATA
* *
49109616 A--TACACAACTGACATAA
1 ACTTACATAACTTACAT-A
49109633 ACTTACATAA--TACATA
1 ACTTACATAACTTACATA
** *
49109649 TTTTACATCACTTACATA
1 ACTTACATAACTTACATA
*
49109667 A--GACATAACTTACATA
1 ACTTACATAACTTACATA
* * *
49109683 AGTTTCATAA--TACACA
1 ACTTACATAACTTACATA
*
49109699 ACTAACATAACTTACATA
1 ACTTACATAACTTACATA
*
49109717 A--TACACAACTTACATA
1 ACTTACATAACTTACATA
* *
49109733 AC-CATCATAA--TACACA
1 ACTTA-CATAACTTACATA
* *
49109749 ACTTACATAAGTTTCATA
1 ACTTACATAACTTACATA
*
49109767 A--TACACAACTTACATA
1 ACTTACATAACTTACATA
* *
49109783 GCTTACATAACTTACACA
1 ACTTACATAACTTACATA
49109801 ACTTACATAACTTACATA
1 ACTTACATAACTTACATA
49109819 A
1 A
49109820 TAAATAAGTT
Statistics
Matches: 194, Mismatches: 42, Indels: 36
0.71 0.15 0.13
Matches are distributed among these distances:
16 109 0.56
17 8 0.04
18 71 0.37
19 6 0.03
ACGTcount: A:0.47, C:0.21, G:0.02, T:0.29
Consensus pattern (18 bp):
ACTTACATAACTTACATA
Found at i:49110637 original size:21 final size:21
Alignment explanation
Indices: 49110612--49110701 Score: 117
Period size: 21 Copynumber: 4.3 Consensus size: 21
49110602 CAGCAACTTA
* * *
49110612 AAGCAGATGCGGCAGCGAGGG
1 AAGCAGAGGCCGCAGCGAGAG
* ** *
49110633 AAGCAGCGGCTACAGTGAGAG
1 AAGCAGAGGCCGCAGCGAGAG
49110654 AAGCAGAGGCCGCAGCGAGAG
1 AAGCAGAGGCCGCAGCGAGAG
49110675 AAGCAGAGGCCGCAGCGAGAG
1 AAGCAGAGGCCGCAGCGAGAG
49110696 AAGCAG
1 AAGCAG
49110702 CGAGAGANNN
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 59 1.00
ACGTcount: A:0.33, C:0.21, G:0.42, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCCGCAGCGAGAG
Found at i:49111480 original size:42 final size:42
Alignment explanation
Indices: 49111187--49111491 Score: 303
Period size: 42 Copynumber: 7.2 Consensus size: 42
49111177 GTTTTTGAAC
* **
49111187 TAAGCGCCGCTAAAGAACACT-A-CTTTTAGCGGCATTTTTGAA
1 TAAGCGCCGCTAAAGAACA-TGATC-TTTAGCGGCGTTTTTTTA
* * * * * *
49111229 CAAGCGCCGCTATAGAACATTA-CTTTTAG-AGCGTTTTCCTCA
1 TAAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGTTTT-TTTA
* * *
49111271 AAAGCGCCGCTAAAGAACATGAACTTTAGCGGCGTTTTTTTCC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT-A
* * * *
49111314 TAAGCGCCGTTAAAGAACATGATATTTAGCGGCGTTTATTTC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTA
** * * *
49111356 TAAGCGCCGCTAAAGATTATGTTCTTTAGCGGCGTTTATTTG
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTA
* **
49111398 TAAGCGCCACTAAAGAACATGATCTTTAGCGGCGCATTTTTA
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTA
49111440 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTA
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTA
49111482 TGTAAGCGCC
1 --TAAGCGCC
49111492 ACAAAAGTTA
Statistics
Matches: 220, Mismatches: 36, Indels: 12
0.82 0.13 0.04
Matches are distributed among these distances:
41 7 0.03
42 161 0.73
43 44 0.20
44 8 0.04
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (42 bp):
TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTA
Found at i:49111601 original size:22 final size:22
Alignment explanation
Indices: 49111570--49111612 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
49111560 TAGTGGCGTT
* *
49111570 AAAAAGCGCCGCTAAAGACCTA
1 AAAAAACGCCGCTAAAAACCTA
49111592 AAAAAACGCCGCTAAAAACCT
1 AAAAAACGCCGCTAAAAACCT
49111613 GTTCTGCTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.49, C:0.28, G:0.14, T:0.09
Consensus pattern (22 bp):
AAAAAACGCCGCTAAAAACCTA
Found at i:49112879 original size:11 final size:11
Alignment explanation
Indices: 49112865--49112905 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
49112855 TGTTTTCTCC
49112865 CTATTTTGCTA
1 CTATTTTGCTA
*
49112876 CTATTTTACTA
1 CTATTTTGCTA
* *
49112887 TTATGTTGCTA
1 CTATTTTGCTA
49112898 CTATTTTG
1 CTATTTTG
49112906 TTGTTATTGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:49112976 original size:30 final size:30
Alignment explanation
Indices: 49112942--49113006 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
49112932 ACTTATTTTA
*
49112942 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTACTTTAAAGGCAT
*
49112972 TTGTTAATTTTGTTATTACTTTAGAGGCAT
1 TTGTTAATTTTGTTATTACTTTAAAGGCAT
49113002 TTGTT
1 TTGTT
49113007 TGTTAAGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.23, C:0.05, G:0.15, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTACTTTAAAGGCAT
Found at i:49117419 original size:4 final size:4
Alignment explanation
Indices: 49117410--49117448 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
49117400 AACTAAGTAA
49117410 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
49117449 AATAAAACTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:49123935 original size:18 final size:19
Alignment explanation
Indices: 49123890--49123938 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
49123880 GAATATTTAC
*
49123890 ATAAAAATTAAACTAAGTAA
1 ATAAAAA-TAAACTAAATAA
49123910 A-AATAAATAAA-TAAATAA
1 ATAA-AAATAAACTAAATAA
49123928 ATAAAAATAAA
1 ATAAAAATAAA
49123939 ACTTTACAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 14 0.54
19 8 0.31
20 4 0.15
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (19 bp):
ATAAAAATAAACTAAATAA
Found at i:49132005 original size:40 final size:39
Alignment explanation
Indices: 49131944--49132076 Score: 158
Period size: 40 Copynumber: 3.3 Consensus size: 39
49131934 TTATACTTTT
* * * *
49131944 TGTTTGGCGTGTTTCGATTGGACCAACTCTTATGAGCTTC
1 TGTTTGGTGTGTTTTGGTTGGA-TAACTCTTATGAGCTTC
49131984 TGTTTGGTGTGTTTTGGTTGGATAAGCTCTTATGAGCTTC
1 TGTTTGGTGTGTTTTGGTTGGATAA-CTCTTATGAGCTTC
* * * *
49132024 TTTTTGGTGTGTTTTGGTTGGATTAGCTATTATGTGCTTC
1 TGTTTGGTGTGTTTTGGTTGGA-TAACTCTTATGAGCTTC
*
49132064 TGTCTGGTGTGTT
1 TGTTTGGTGTGTT
49132077 CGGTTGATCT
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
39 2 0.02
40 77 0.95
41 2 0.02
ACGTcount: A:0.11, C:0.12, G:0.29, T:0.48
Consensus pattern (39 bp):
TGTTTGGTGTGTTTTGGTTGGATAACTCTTATGAGCTTC
Found at i:49133766 original size:18 final size:18
Alignment explanation
Indices: 49133743--49133780 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
49133733 TGACTTACAC
*
49133743 GGGCACGGGCATGGGCTG
1 GGGCACGGGCACGGGCTG
49133761 GGGCACGGGCACGGGCTG
1 GGGCACGGGCACGGGCTG
49133779 GG
1 GG
49133781 ACACAGGCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.11, C:0.24, G:0.58, T:0.08
Consensus pattern (18 bp):
GGGCACGGGCACGGGCTG
Found at i:49139141 original size:9 final size:9
Alignment explanation
Indices: 49139098--49139141 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
49139088 AATCGAAGAA
*
49139098 TCATCATCC
1 TCATCATTC
*
49139107 TCATCATCC
1 TCATCATTC
* *
49139116 TCATCCTTA
1 TCATCATTC
49139125 TCATCATTC
1 TCATCATTC
49139134 TCATCATT
1 TCATCATT
49139142 GCAATCAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.23, C:0.36, G:0.00, T:0.41
Consensus pattern (9 bp):
TCATCATTC
Found at i:49140708 original size:18 final size:17
Alignment explanation
Indices: 49140677--49140711 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
49140667 AGGTAGCCAA
49140677 CTCTTCTTTAACATAAT
1 CTCTTCTTTAACATAAT
*
49140694 CTCTCTCTTTTACATAAT
1 CTCT-TCTTTAACATAAT
49140712 ACATTTGGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.49
Consensus pattern (17 bp):
CTCTTCTTTAACATAAT
Found at i:49140982 original size:19 final size:19
Alignment explanation
Indices: 49140958--49140997 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
49140948 AAAAATATTT
49140958 AATTATAATTAAATAATTA
1 AATTATAATTAAATAATTA
* *
49140977 AATTATACTTAAATTATTA
1 AATTATAATTAAATAATTA
49140996 AA
1 AA
49140998 ATTTTTAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
AATTATAATTAAATAATTA
Found at i:49142012 original size:20 final size:22
Alignment explanation
Indices: 49141983--49142029 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
49141973 AAATTAATGT
49141983 TAATATATATAAAAATTGAATC
1 TAATATATATAAAAATTGAATC
*
49142005 TAATATATATAAAAATTGGATC
1 TAATATATATAAAAATTGAATC
49142027 TAA
1 TAA
49142030 CCATGGAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.53, C:0.04, G:0.06, T:0.36
Consensus pattern (22 bp):
TAATATATATAAAAATTGAATC
Found at i:49144774 original size:24 final size:24
Alignment explanation
Indices: 49144723--49144774 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
49144713 TCACTTTACC
***
49144723 AAAAAATTAAAATAAATATTTCTG
1 AAAAAATTAAAATAAATATTTAAA
49144747 AAAAAATTGAAAATAAAT-TTTAAA
1 AAAAAATT-AAAATAAATATTTAAA
49144771 AAAA
1 AAAA
49144775 TATGTCTACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 15 0.62
25 9 0.38
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (24 bp):
AAAAAATTAAAATAAATATTTAAA
Found at i:49171336 original size:55 final size:55
Alignment explanation
Indices: 49171270--49171379 Score: 211
Period size: 55 Copynumber: 2.0 Consensus size: 55
49171260 TAATTTATGA
*
49171270 TCAAAAACGTCTTCTGAATGTTTAAACCAACTTTCTCATTTTTAGCTGTGCATTC
1 TCAAAAACGTCTTCGGAATGTTTAAACCAACTTTCTCATTTTTAGCTGTGCATTC
49171325 TCAAAAACGTCTTCGGAATGTTTAAACCAACTTTCTCATTTTTAGCTGTGCATTC
1 TCAAAAACGTCTTCGGAATGTTTAAACCAACTTTCTCATTTTTAGCTGTGCATTC
49171380 ACAACTCAAA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (55 bp):
TCAAAAACGTCTTCGGAATGTTTAAACCAACTTTCTCATTTTTAGCTGTGCATTC
Found at i:49173300 original size:22 final size:20
Alignment explanation
Indices: 49173275--49173314 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
49173265 TTTGTTAGAA
49173275 TTTAATGTTATATAAAATTGCC
1 TTTAAT-TTATA-AAAATTGCC
*
49173297 TTTAATTTTTAAAAATTG
1 TTTAATTTATAAAAATTG
49173315 AGTGTAGTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 4 0.24
22 6 0.35
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (20 bp):
TTTAATTTATAAAAATTGCC
Found at i:49173595 original size:23 final size:24
Alignment explanation
Indices: 49173552--49173596 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
49173542 GTGAAGCTCA
* *
49173552 AAAAACGCTTCCAATTGGAAGCCT
1 AAAAACGCTTCCAACTAGAAGCCT
49173576 AAAAAC-CTTCCAACTAGAAGC
1 AAAAACGCTTCCAACTAGAAGC
49173597 TTTTTCATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.42, C:0.27, G:0.13, T:0.18
Consensus pattern (24 bp):
AAAAACGCTTCCAACTAGAAGCCT
Found at i:49174849 original size:21 final size:21
Alignment explanation
Indices: 49174807--49174850 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
49174797 TCATATAGTC
* **
49174807 AAGTATCGATGCCAAATGTCA
1 AAGTATCGATACCAAACATCA
*
49174828 AAGTATCGATACCTAACATCA
1 AAGTATCGATACCAAACATCA
49174849 AA
1 AA
49174851 ATGGTAAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.23
Consensus pattern (21 bp):
AAGTATCGATACCAAACATCA
Found at i:49177792 original size:13 final size:13
Alignment explanation
Indices: 49177774--49177839 Score: 89
Period size: 13 Copynumber: 5.1 Consensus size: 13
49177764 AGTTCTTCAT
49177774 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
49177787 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
49177800 TG-TTGTGGAAAAG
1 TGCTT-TTGAAAAG
*
49177813 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
*
49177826 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
49177839 T
1 T
49177840 TTGGTTTAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
12 2 0.04
13 44 0.92
14 2 0.04
ACGTcount: A:0.27, C:0.06, G:0.29, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:49179034 original size:13 final size:13
Alignment explanation
Indices: 49179016--49179048 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
49179006 AGTTAATTTA
*
49179016 AAATTTATGAAAT
1 AAATTTATAAAAT
49179029 AAATTTA-AAAAT
1 AAATTTATAAAAT
49179041 AAATTTAT
1 AAATTTAT
49179049 TAATTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (13 bp):
AAATTTATAAAAT
Found at i:49179464 original size:33 final size:33
Alignment explanation
Indices: 49179422--49179500 Score: 131
Period size: 33 Copynumber: 2.4 Consensus size: 33
49179412 GTCGCCTGCT
49179422 GCTCACCAATCACCACCACCGCTATCCAGCGTC
1 GCTCACCAATCACCACCACCGCTATCCAGCGTC
*
49179455 GCTCACCAATCACCACCACCGCTGTCCAGCGTC
1 GCTCACCAATCACCACCACCGCTATCCAGCGTC
* *
49179488 ACTCACCACTCAC
1 GCTCACCAATCAC
49179501 TAGTCACCAC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.24, C:0.49, G:0.11, T:0.15
Consensus pattern (33 bp):
GCTCACCAATCACCACCACCGCTATCCAGCGTC
Found at i:49184967 original size:12 final size:12
Alignment explanation
Indices: 49184950--49184980 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
49184940 CTCCAGTTTT
49184950 CACACGGCCTAA
1 CACACGGCCTAA
*
49184962 CACACGGCCTAG
1 CACACGGCCTAA
49184974 CACACGG
1 CACACGG
49184981 GTGTGTGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.42, G:0.23, T:0.06
Consensus pattern (12 bp):
CACACGGCCTAA
Found at i:49188583 original size:34 final size:32
Alignment explanation
Indices: 49188534--49188613 Score: 88
Period size: 34 Copynumber: 2.4 Consensus size: 32
49188524 AGAATAAGGG
* **
49188534 AAAATAAAAAGAAAAGTTATTGATGAAAGAAAA
1 AAAAGAAAAAGAAAAGACATTGA-GAAAGAAAA
* *
49188567 TAAAAGAAAAATAAAAGACATTGAGAGAGAAAA
1 -AAAAGAAAAAGAAAAGACATTGAGAAAGAAAA
*
49188600 AAAAGAAAAGGAAA
1 AAAAGAAAAAGAAA
49188614 TAAAAAGAGA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
32 12 0.31
33 8 0.21
34 19 0.49
ACGTcount: A:0.69, C:0.01, G:0.17, T:0.12
Consensus pattern (32 bp):
AAAAGAAAAAGAAAAGACATTGAGAAAGAAAA
Found at i:49191374 original size:12 final size:12
Alignment explanation
Indices: 49191357--49191381 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
49191347 AATTTAATAG
49191357 ATTTAATATTAA
1 ATTTAATATTAA
49191369 ATTTAATATTAA
1 ATTTAATATTAA
49191381 A
1 A
49191382 GTGATTAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTTAATATTAA
Found at i:49202099 original size:21 final size:21
Alignment explanation
Indices: 49202037--49202234 Score: 130
Period size: 21 Copynumber: 9.4 Consensus size: 21
49202027 GAAGCCCGAA
* *
49202037 AGTTGAACAAAAGCTCATGAG
1 AGTTGAACAGAAGCTCATAAG
* * * * *
49202058 AGCTAAATAGAAACCCATAAG
1 AGTTGAACAGAAGCTCATAAG
* *
49202079 GGTTGAACAGAAGCTCGTAAG
1 AGTTGAACAGAAGCTCATAAG
* *
49202100 AGTTGAAC-GAAAACCCATAAG
1 AGTTGAACAG-AAGCTCATAAG
* * * *
49202121 AGTTAAATAGAAGCTCAAAAT
1 AGTTGAACAGAAGCTCATAAG
*
49202142 AGTTGAACAGAAAC-CTATAAG
1 AGTTGAACAGAAGCTC-ATAAG
* * *
49202163 GGTTAAACAGAAGCTCAAAAG
1 AGTTGAACAGAAGCTCATAAG
* *
49202184 AGTTGAACAGAAACCCATAAG
1 AGTTGAACAGAAGCTCATAAG
* * * *
49202205 GGTTAAACAAAAGCTCAAAAG
1 AGTTGAACAGAAGCTCATAAG
*
49202226 AGCTGAACA
1 AGTTGAACA
49202235 AAAAGTAAAC
Statistics
Matches: 126, Mismatches: 47, Indels: 8
0.70 0.26 0.04
Matches are distributed among these distances:
20 2 0.02
21 122 0.97
22 2 0.02
ACGTcount: A:0.47, C:0.16, G:0.21, T:0.17
Consensus pattern (21 bp):
AGTTGAACAGAAGCTCATAAG
Found at i:49202114 original size:42 final size:42
Alignment explanation
Indices: 49202066--49202234 Score: 241
Period size: 42 Copynumber: 4.0 Consensus size: 42
49202056 AGAGCTAAAT
* **
49202066 AGAAACCCATAAGGGTTGAACAGAAGCTCGTAAGAGTTGAAC
1 AGAAACCCATAAGGGTTAAACAGAAGCTCAAAAGAGTTGAAC
* * *
49202108 -GAAAACCCATAAGAGTTAAATAGAAGCTCAAAATAGTTGAAC
1 AG-AAACCCATAAGGGTTAAACAGAAGCTCAAAAGAGTTGAAC
*
49202150 AGAAACCTATAAGGGTTAAACAGAAGCTCAAAAGAGTTGAAC
1 AGAAACCCATAAGGGTTAAACAGAAGCTCAAAAGAGTTGAAC
* *
49202192 AGAAACCCATAAGGGTTAAACAAAAGCTCAAAAGAGCTGAAC
1 AGAAACCCATAAGGGTTAAACAGAAGCTCAAAAGAGTTGAAC
49202234 A
1 A
49202235 AAAAGTAAAC
Statistics
Matches: 112, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
41 1 0.01
42 110 0.98
43 1 0.01
ACGTcount: A:0.47, C:0.16, G:0.21, T:0.16
Consensus pattern (42 bp):
AGAAACCCATAAGGGTTAAACAGAAGCTCAAAAGAGTTGAAC
Found at i:49202188 original size:84 final size:84
Alignment explanation
Indices: 49202037--49202234 Score: 254
Period size: 84 Copynumber: 2.4 Consensus size: 84
49202027 GAAGCCCGAA
* ** * * * **
49202037 AGTTGAACAAAAGCTCATGAGAGCTAAATAGAAACCCATAAGGGTTGAACAGAAGCTCGTAAGAG
1 AGTTAAACAAAAGCTCAAAAGAGCTGAACAGAAACCCATAAGGGTTAAACAGAAGCTCAAAAGAG
49202102 TTGAAC-GAAAACCCATAAG
66 TTGAACAG-AAACCCATAAG
* * * * *
49202121 AGTTAAATAGAAGCTCAAAATAGTTGAACAGAAACCTATAAGGGTTAAACAGAAGCTCAAAAGAG
1 AGTTAAACAAAAGCTCAAAAGAGCTGAACAGAAACCCATAAGGGTTAAACAGAAGCTCAAAAGAG
49202186 TTGAACAGAAACCCATAAG
66 TTGAACAGAAACCCATAAG
*
49202205 GGTTAAACAAAAGCTCAAAAGAGCTGAACA
1 AGTTAAACAAAAGCTCAAAAGAGCTGAACA
49202235 AAAAGTAAAC
Statistics
Matches: 95, Mismatches: 18, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
84 94 0.99
85 1 0.01
ACGTcount: A:0.47, C:0.16, G:0.21, T:0.17
Consensus pattern (84 bp):
AGTTAAACAAAAGCTCAAAAGAGCTGAACAGAAACCCATAAGGGTTAAACAGAAGCTCAAAAGAG
TTGAACAGAAACCCATAAG
Found at i:49202236 original size:21 final size:21
Alignment explanation
Indices: 49202080--49202275 Score: 102
Period size: 21 Copynumber: 9.5 Consensus size: 21
49202070 ACCCATAAGG
* **
49202080 GTTGAACAGAAGCTCGTAAGA
1 GTTGAACAAAAGCTCAAAAGA
* *
49202101 GTTGAACGAAAA-CCCATAAGA
1 GTTGAAC-AAAAGCTCAAAAGA
* * * *
49202122 GTTAAATAGAAGCTCAAAATA
1 GTTGAACAAAAGCTCAAAAGA
* * *
49202143 GTTGAACAGAAACCT-ATAAGG
1 GTTGAACA-AAAGCTCAAAAGA
* *
49202164 GTTAAACAGAAGCTCAAAAGA
1 GTTGAACAAAAGCTCAAAAGA
* * *
49202185 GTTGAACAGAAA-CCCATAAGG
1 GTTGAACA-AAAGCTCAAAAGA
*
49202206 GTTAAACAAAAGCTCAAAAGA
1 GTTGAACAAAAGCTCAAAAGA
* *
49202227 GCTGAACAAAAAG-T--AAACA
1 GTTGAAC-AAAAGCTCAAAAGA
* *
49202246 --CGAACAGAAGCTCAAAAGA
1 GTTGAACAAAAGCTCAAAAGA
49202265 GTTGAACAAAA
1 GTTGAACAAAA
49202276 AGTAAACACG
Statistics
Matches: 125, Mismatches: 38, Indels: 24
0.67 0.20 0.13
Matches are distributed among these distances:
16 4 0.03
17 5 0.04
19 8 0.06
20 10 0.08
21 84 0.67
22 14 0.11
ACGTcount: A:0.49, C:0.15, G:0.20, T:0.15
Consensus pattern (21 bp):
GTTGAACAAAAGCTCAAAAGA
Found at i:49202271 original size:38 final size:38
Alignment explanation
Indices: 49202210--49202286 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
49202200 ATAAGGGTTA
49202210 AACAAAAGCTCAAAAGAGCTGAACAAAAAGTAAACACG
1 AACAAAAGCTCAAAAGAGCTGAACAAAAAGTAAACACG
* *
49202248 AACAGAAGCTCAAAAGAGTTGAACAAAAAGTAAACACG
1 AACAAAAGCTCAAAAGAGCTGAACAAAAAGTAAACACG
49202286 A
1 A
49202287 GAGTTCGCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.57, C:0.17, G:0.17, T:0.09
Consensus pattern (38 bp):
AACAAAAGCTCAAAAGAGCTGAACAAAAAGTAAACACG
Found at i:49207023 original size:6 final size:6
Alignment explanation
Indices: 49207012--49207045 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
49207002 AGGTTTCTCA
*
49207012 AAATGG AAATGG AAATGG AAATGG AAATGA AAAT
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAAT
49207046 AAAAAATGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.56, C:0.00, G:0.26, T:0.18
Consensus pattern (6 bp):
AAATGG
Found at i:49209406 original size:137 final size:138
Alignment explanation
Indices: 49209254--49209554 Score: 403
Period size: 146 Copynumber: 2.2 Consensus size: 138
49209244 AAAAAAGAGC
*
49209254 TTAGATTTTTAAAATAAAAATATTTTTTTTAGTCATATTAAA-G-G-AAAAATTTAAAACAAAGT
1 TTAGATTTTTAAAATAAAAATATGTTTTTTAGTCATATTAAATGAGTAAAAATTTAAAACAAAGT
* *
49209316 TTTGAT-TTTTTCAACTATTTCGAAATAAATCTTTGATTTTTATGAAAAATAGTGATTTTTTTAA
66 TTTGATATTTTTCAACTATTTCGAAATAAAGCTTTGATTTTTAAGAAAAATAGTGATTTTTTT-A
49209380 AAAGAGAAAGT
130 AAAGA-AAA-T
* *
49209391 TTAGATTTTTAAAATAAAAATATGTTTTTTAGTCATTTTAAATGAAAAGTTTAAAATTTTAAAAC
1 TTAGATTTTTAAAATAAAAATATGTTTTTTAGTCATATTAAATG---AG--TAAAAATTTAAAAC
* *
49209456 AAAGTTTTGATATTTTTCAATTATTTCGAAATAAAGCTTTGATTTTTAAGAAAATTAGTGATTTT
61 AAAGTTTTGATATTTTTCAACTATTTCGAAATAAAGCTTTGATTTTTAAGAAAAATAGTGATTTT
*
49209521 TTTTAAAGAAAAT
126 TTTAAAAGAAAAT
* * *
49209534 TTTGATTTTGAAAAAAAAAAT
1 TTAGATTTTTAAAATAAAAAT
49209555 TTCAGCCACT
Statistics
Matches: 144, Mismatches: 11, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
137 40 0.28
138 1 0.01
142 1 0.01
143 19 0.13
144 3 0.02
145 28 0.19
146 52 0.36
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.44
Consensus pattern (138 bp):
TTAGATTTTTAAAATAAAAATATGTTTTTTAGTCATATTAAATGAGTAAAAATTTAAAACAAAGT
TTTGATATTTTTCAACTATTTCGAAATAAAGCTTTGATTTTTAAGAAAAATAGTGATTTTTTTAA
AAGAAAAT
Found at i:49209524 original size:23 final size:22
Alignment explanation
Indices: 49209498--49209542 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
49209488 AAAGCTTTGA
49209498 TTTTT-AAGAAAATTAGTGATTT
1 TTTTTAAAGAAAATT-GTGATTT
*
49209520 TTTTTAAAGAAAATTTTGATTT
1 TTTTTAAAGAAAATTGTGATTT
49209542 T
1 T
49209543 GAAAAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (22 bp):
TTTTTAAAGAAAATTGTGATTT
Found at i:49210099 original size:21 final size:21
Alignment explanation
Indices: 49210066--49210117 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 21
49210056 ATGTTTTATA
* * * *
49210066 TTTATTCACTCTTGTATAATT
1 TTTATTTATTCTTATATAATC
* *
49210087 TTTATTTATTCTTATTTCATC
1 TTTATTTATTCTTATATAATC
49210108 TTTATTTATT
1 TTTATTTATT
49210118 TTCATGTCCA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.21, C:0.12, G:0.02, T:0.65
Consensus pattern (21 bp):
TTTATTTATTCTTATATAATC
Found at i:49225011 original size:12 final size:12
Alignment explanation
Indices: 49224994--49225056 Score: 99
Period size: 12 Copynumber: 5.0 Consensus size: 12
49224984 GTTGATTGTG
49224994 TTATTGTTTGAA
1 TTATTGTTTGAA
49225006 TTATTGTGTTTGAA
1 TTA-T-TGTTTGAA
49225020 TTATTGTTTGAA
1 TTATTGTTTGAA
49225032 TTATTGTTTGAA
1 TTATTGTTTGAA
49225044 TTATTGTGTTGAA
1 TTATTGT-TTGAA
49225057 GCTTTCGGCA
Statistics
Matches: 48, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
12 30 0.62
13 7 0.15
14 11 0.23
ACGTcount: A:0.24, C:0.00, G:0.19, T:0.57
Consensus pattern (12 bp):
TTATTGTTTGAA
Found at i:49226352 original size:26 final size:27
Alignment explanation
Indices: 49226316--49226366 Score: 95
Period size: 26 Copynumber: 1.9 Consensus size: 27
49226306 AGAATATGAT
49226316 TTTGAATTTGTTATAGC-ATGCTCTTG
1 TTTGAATTTGTTATAGCAATGCTCTTG
49226342 TTTGAATTTGTTATAGCAATGCTCT
1 TTTGAATTTGTTATAGCAATGCTCT
49226367 AACCATTGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.49
Consensus pattern (27 bp):
TTTGAATTTGTTATAGCAATGCTCTTG
Found at i:49234882 original size:18 final size:18
Alignment explanation
Indices: 49234859--49234898 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
49234849 TCTTGTCACC
*
49234859 AAATATTTTGAAAT-TAAA
1 AAATATATT-AAATGTAAA
49234877 AAATATATTAAATGTAAA
1 AAATATATTAAATGTAAA
49234895 AAAT
1 AAAT
49234899 TTGATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (18 bp):
AAATATATTAAATGTAAA
Found at i:49235141 original size:52 final size:52
Alignment explanation
Indices: 49235067--49235167 Score: 150
Period size: 52 Copynumber: 1.9 Consensus size: 52
49235057 AAAAGTTTTT
*
49235067 AGGGTTTAGGGGAAAGTTAAAGTTTTAGGAGGAAAGCAAAAGGGAAAAAATTG
1 AGGGTTTAGGGGAAAGTAAAAGTTTTAGGAGGAAAGCAAAA-GGAAAAAATTG
* * *
49235120 AGGGTTT-GGGGAAAGTAAAAGTTTTAGGGGGAAAGTAACAGGAAAAAA
1 AGGGTTTAGGGGAAAGTAAAAGTTTTAGGAGGAAAGCAAAAGGAAAAAA
49235168 GTTTTGGGGG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 8 0.18
52 29 0.66
53 7 0.16
ACGTcount: A:0.44, C:0.02, G:0.35, T:0.20
Consensus pattern (52 bp):
AGGGTTTAGGGGAAAGTAAAAGTTTTAGGAGGAAAGCAAAAGGAAAAAATTG
Found at i:49237936 original size:31 final size:29
Alignment explanation
Indices: 49237879--49237936 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
49237869 AAATCAGCAA
* *
49237879 CAAAAGAAAAAGATGGAAATGCCAGAACC
1 CAAAAGAAAAAGAAGGAAATGACAGAACC
49237908 CAAAAGAAAAAGAAGGAAAAATGACAGAA
1 CAAAAGAAAAAGAAGG--AAATGACAGAA
49237937 AGGGAATCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 15 0.60
31 10 0.40
ACGTcount: A:0.62, C:0.12, G:0.21, T:0.05
Consensus pattern (29 bp):
CAAAAGAAAAAGAAGGAAATGACAGAACC
Found at i:49242687 original size:13 final size:13
Alignment explanation
Indices: 49242669--49242714 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
49242659 ACTAAATTTG
49242669 ATTAAGGTTAATT
1 ATTAAGGTTAATT
49242682 ATTAAGGTTAATT
1 ATTAAGGTTAATT
**
49242695 AGTTAATTTTAATT
1 A-TTAAGGTTAATT
49242709 AATTAA
1 -ATTAA
49242715 TAAAATAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 14 0.48
14 14 0.48
15 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (13 bp):
ATTAAGGTTAATT
Found at i:49243065 original size:20 final size:20
Alignment explanation
Indices: 49243028--49243065 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
49243018 AGGGTTAAAG
*
49243028 TGTATAAATTTTAAAATTCA
1 TGTATAAATTTCAAAATTCA
49243048 TGTA-AAATTTCAATAATT
1 TGTATAAATTTCAA-AATT
49243066 ATAGACAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (20 bp):
TGTATAAATTTCAAAATTCA
Found at i:49247581 original size:25 final size:26
Alignment explanation
Indices: 49247546--49247602 Score: 107
Period size: 25 Copynumber: 2.2 Consensus size: 26
49247536 AAGCTCATGT
49247546 ATCTCACATACAACCCTAAACTTACC
1 ATCTCACATACAACCCTAAACTTACC
49247572 ATCTC-CATACAACCCTAAACTTACC
1 ATCTCACATACAACCCTAAACTTACC
49247597 ATCTCA
1 ATCTCA
49247603 AATTTCAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 25 0.83
26 5 0.17
ACGTcount: A:0.37, C:0.39, G:0.00, T:0.25
Consensus pattern (26 bp):
ATCTCACATACAACCCTAAACTTACC
Found at i:49247719 original size:17 final size:17
Alignment explanation
Indices: 49247697--49247730 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
49247687 AACTCGACCC
49247697 ATTCTATAATTTGAATT
1 ATTCTATAATTTGAATT
49247714 ATTCTATAATTTGAATT
1 ATTCTATAATTTGAATT
49247731 GCTTAATCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (17 bp):
ATTCTATAATTTGAATT
Found at i:49251521 original size:21 final size:21
Alignment explanation
Indices: 49251496--49251589 Score: 135
Period size: 19 Copynumber: 4.7 Consensus size: 21
49251486 AAATTTGAGG
49251496 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
49251517 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
49251538 ATA--CAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
49251557 ATAT--AATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
* *
49251576 -TTTGTAATCTTAGA
1 ATATGCAATCTTAGA
49251590 GATTTAATTT
Statistics
Matches: 69, Mismatches: 1, Indels: 7
0.90 0.01 0.09
Matches are distributed among these distances:
18 2 0.03
19 34 0.49
20 9 0.13
21 24 0.35
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:49251539 original size:40 final size:38
Alignment explanation
Indices: 49251495--49251589 Score: 136
Period size: 40 Copynumber: 2.4 Consensus size: 38
49251485 TAAATTTGAG
49251495 GATATGCAATCTTAGATATGATATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATATGATATAT--AATCTTAGATAT
*
49251535 GATATACAATCTTAGATATGATATATAATCTTAGATAT
1 GATATGCAATCTTAGATATGATATATAATCTTAGATAT
* *
49251573 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
49251590 GATTTAATTT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
38 14 0.28
39 11 0.22
40 25 0.50
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.40
Consensus pattern (38 bp):
GATATGCAATCTTAGATATGATATATAATCTTAGATAT
Found at i:49253089 original size:98 final size:98
Alignment explanation
Indices: 49252968--49253158 Score: 355
Period size: 98 Copynumber: 1.9 Consensus size: 98
49252958 ATAATAAATG
*
49252968 AAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTCTTAAAT
1 AAATATTCCGAGTTTGGGATTTTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTTAAAT
49253033 CTTGGATAAGTGGATGTTCTTTTAAAGTAAAGA
66 CTTGGATAAGTGGATGTTCTTTTAAAGTAAAGA
* *
49253066 AAATATTTCGAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTTAAAT
1 AAATATTCCGAGTTTGGGATTTTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTTAAAT
49253131 CTTGGATAAGTGGATGTTCTTTTAAAGT
66 CTTGGATAAGTGGATGTTCTTTTAAAGT
49253159 TTTATTGTAC
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 90 1.00
ACGTcount: A:0.28, C:0.09, G:0.24, T:0.39
Consensus pattern (98 bp):
AAATATTCCGAGTTTGGGATTTTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTTAAAT
CTTGGATAAGTGGATGTTCTTTTAAAGTAAAGA
Found at i:49255293 original size:39 final size:41
Alignment explanation
Indices: 49255223--49255311 Score: 112
Period size: 39 Copynumber: 2.2 Consensus size: 41
49255213 GTCAACATTT
* **
49255223 AATTAATTTTTAAAAACTTTAAAATTGTTAAAAAAT-TAAAA
1 AATT-ATTTTTAAAAACATTAAAATCATTAAAAAATATAAAA
*
49255264 AATTATTTTTAAAAA-ATTAAAATCATTAAAAAGTATAAAA
1 AATTATTTTTAAAAACATTAAAATCATTAAAAAATATAAAA
49255304 AA-TATTTT
1 AATTATTTT
49255312 AAACATTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
39 21 0.49
40 18 0.42
41 4 0.09
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (41 bp):
AATTATTTTTAAAAACATTAAAATCATTAAAAAATATAAAA
Found at i:49256237 original size:88 final size:88
Alignment explanation
Indices: 49256088--49256250 Score: 231
Period size: 88 Copynumber: 1.9 Consensus size: 88
49256078 GGAGACTGCA
* * *
49256088 TGCTCCGCAGGCAACCTAGAGTGAAACACGTGTCCAACAGGCCTGAAACCCATGCGAAATGCCTG
1 TGCTCCGCAGGCAACCCAAAGTGAAACACGTGTCCAACAGGCCTGAAACCCATGCGAAATGCCAG
49256153 TACTAGGAACAAAAAGGATCGAG
66 TACTAGGAACAAAAAGGATCGAG
* * * *
49256176 TGCTCCGCAGGCAACCCAAAGTGAAACACGTGTCCAGCAGGCCT-AAA-GCTTGCACGGAATGCC
1 TGCTCCGCAGGCAACCCAAAGTGAAACACGTGTCCAACAGGCCTGAAACCCATG--CGAAATGCC
49256239 AGTACTAGGAAC
64 AGTACTAGGAAC
49256251 GGTGGAGTTA
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
86 3 0.05
87 3 0.05
88 60 0.91
ACGTcount: A:0.33, C:0.28, G:0.25, T:0.15
Consensus pattern (88 bp):
TGCTCCGCAGGCAACCCAAAGTGAAACACGTGTCCAACAGGCCTGAAACCCATGCGAAATGCCAG
TACTAGGAACAAAAAGGATCGAG
Found at i:49261340 original size:2 final size:2
Alignment explanation
Indices: 49261333--49261374 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
49261323 TTAAACTAGA
49261333 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
49261375 GGAAATCTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49262006 original size:41 final size:41
Alignment explanation
Indices: 49261961--49262063 Score: 134
Period size: 41 Copynumber: 2.5 Consensus size: 41
49261951 GGCTATGTGC
* *
49261961 CTAGCAGGCTTAATGCCGGTGAAATAATTCAGACTTTACGT
1 CTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATACGT
* * * *
49262002 CTAGCAGGCTTAATGCCGGTGATACATTTCGGACTATAGGT
1 CTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATACGT
* *
49262043 CTAGCAGGCTAAAAGCCGGTG
1 CTAGCAGGCTTAATGCCGGTG
49262064 TATCGAATCA
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.26
Consensus pattern (41 bp):
CTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATACGT
Found at i:49262513 original size:2 final size:2
Alignment explanation
Indices: 49262506--49262531 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
49262496 ATAATGAGTG
49262506 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
49262532 CACAAACGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:49262844 original size:10 final size:10
Alignment explanation
Indices: 49262820--49262861 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
49262810 ACCAGGAAAT
*
49262820 TTTATA-ATT
1 TTTATATATA
49262829 TTTATATATA
1 TTTATATATA
49262839 TTTATATATA
1 TTTATATATA
49262849 --TATATATA
1 TTTATATATA
49262857 TTTAT
1 TTTAT
49262862 GGTTATGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
8 8 0.28
9 6 0.21
10 15 0.52
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TTTATATATA
Found at i:49263251 original size:2 final size:2
Alignment explanation
Indices: 49263238--49263277 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
49263228 CCAAGCTTAT
* *
49263238 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TT TA -A TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
49263278 GTATTGAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:49264528 original size:440 final size:440
Alignment explanation
Indices: 49263707--49265027 Score: 2381
Period size: 440 Copynumber: 3.0 Consensus size: 440
49263697 GAATACGATG
* * * *
49263707 TAAAAGAGGCGGTGTTAGACAAATATCATGCTATTGTAGCCTAGTTGCTTGTAGGGTTTGACAAA
1 TAAAAGAGGCGGTGTTAAAGAAATATCATGTTATTGTAGCCTAGTTGCTTGCAGGGTTTGACAAA
* ** * * ** *
49263772 GTTCAGATTAAGCAGCTCCCGAGAAGTGATAACACGCGTGCTGATGCTTTGTCCAAGTTAGCATC
66 GTTCAAATTAAATAGCTCCCGAAAAGTGACAACACATGTGCTAATGCTTTGTCCAAGTTAGCATC
49263837 CTTTGTTGTCATCGAACAAAGAGGGAAAATCCTACTCGAGCATAAAGAGACCCCGAGTTATGACA
131 CTTTGTTGTCATCGAACAAAGAGGGAAAATCCTACTCGAGCATAAAGAGACCCCGAGTTATGACA
49263902 CACTGTAAGTACTATGTATAGATCAAGAAGAAACCTAGATGAATCCAATAGTTTACACTCTCCAA
196 CACTGTAAGTACTATGTATAGATCAAGAAGAAACCTAGATGAATCCAATAGTTTACACTCTCCAA
49263967 GGTGAACAAGATAACCAAGACAAGAAGGAGCTCACGAGGCTACAACTCAAAACTGCGAGGTATGT
261 GGTGAACAAGATAACCAAGACAAGAAGGAGCTCACGAGGCTACAACTCAAAACTGCGAGGTATGT
49264032 CATTATAACAAATTACAAATACCTGTATAACTCCTAATGCGTGAATTGAATATTTGAATGTTGCA
326 CATTATAACAAATTACAAATACCTGTATAACTCCTAATGCGTGAATTGAATATTTGAATGTTGCA
49264097 AACTTGTTTAGTTGCATAATGAATTAAAACAACATATTTTGTCTTATGTT
391 AACTTGTTTAGTTGCATAATGAATTAAAACAACATATTTTGTCTTATGTT
*
49264147 TAAAAGAGGCGGTGTTAAAGAAATATCATGTTATTGTAGCCCAGTTGCTTGCAGGGTTTGACAAA
1 TAAAAGAGGCGGTGTTAAAGAAATATCATGTTATTGTAGCCTAGTTGCTTGCAGGGTTTGACAAA
49264212 GTTCAAATTAAATAGCTCCCGAAAAGTGACAACACATGTGCTAATGCTTTGTCCAAGTTAGCATC
66 GTTCAAATTAAATAGCTCCCGAAAAGTGACAACACATGTGCTAATGCTTTGTCCAAGTTAGCATC
* *
49264277 CTTTGTTGTCATCGAACAAAGAGGGAAAATCCTACTTGAGCATAAAGAGACCCTGAGTTATGACA
131 CTTTGTTGTCATCGAACAAAGAGGGAAAATCCTACTCGAGCATAAAGAGACCCCGAGTTATGACA
49264342 CACTGTAAGTACTATGTATAGATCAAGAAGAAACCTAGATGAATCCAATAGTTTACACTCTCCAA
196 CACTGTAAGTACTATGTATAGATCAAGAAGAAACCTAGATGAATCCAATAGTTTACACTCTCCAA
49264407 GGTGAACAAGATAACCAAGACAAGAAGGAGCTCACGAGGCTACAACTCAAAACTGCGAGGTATGT
261 GGTGAACAAGATAACCAAGACAAGAAGGAGCTCACGAGGCTACAACTCAAAACTGCGAGGTATGT
*
49264472 CATTATAACAAATTACAAATACCTGTATAACTTCTAATGCGTGAATTGAATATTTGAATGTTGCA
326 CATTATAACAAATTACAAATACCTGTATAACTCCTAATGCGTGAATTGAATATTTGAATGTTGCA
* *
49264537 AACTTGTTTAGTTGCATAATGAATTAAAACATCTTATTTTGTCTTATGTT
391 AACTTGTTTAGTTGCATAATGAATTAAAACAACATATTTTGTCTTATGTT
*
49264587 TAAAAGAGGCGGTGTTAAAGAAATATCATATTATTGTAGCCTAGTTGCTTGCAGGGTTTGACAAA
1 TAAAAGAGGCGGTGTTAAAGAAATATCATGTTATTGTAGCCTAGTTGCTTGCAGGGTTTGACAAA
*
49264652 TTTCAAATTAAATAGCTCCCGAAAAGTGACAACACATGTGCTAATGCTTTGTCCAAGTTAGCATC
66 GTTCAAATTAAATAGCTCCCGAAAAGTGACAACACATGTGCTAATGCTTTGTCCAAGTTAGCATC
*
49264717 CTTTGTTGTCATCGAACAAAGAGGGAAAATCCTACTCGAGCATAGAGAGACCCCGAGTTATGACA
131 CTTTGTTGTCATCGAACAAAGAGGGAAAATCCTACTCGAGCATAAAGAGACCCCGAGTTATGACA
* * *
49264782 CACTGTAAGTACTATGCATAGATCAGGAAGAAACCTAGATGAATCCAATAGTTTGCACTCTCCAA
196 CACTGTAAGTACTATGTATAGATCAAGAAGAAACCTAGATGAATCCAATAGTTTACACTCTCCAA
*
49264847 GGTGAACAAGATAACTAAGACAAGAAGGAGCTCACGAGGCTACAACTCAAAACTGCGAGGTATGT
261 GGTGAACAAGATAACCAAGACAAGAAGGAGCTCACGAGGCTACAACTCAAAACTGCGAGGTATGT
* * *
49264912 CATTATAACAAATTACAAATACCTGCATAACTCCTAATGCGTGAATTGAGTATTTGAATATTGCA
326 CATTATAACAAATTACAAATACCTGTATAACTCCTAATGCGTGAATTGAATATTTGAATGTTGCA
*
49264977 AACTTGTTTAGTTGCATAATGAATTAAAACAACATATTTTGTCCTATGTT
391 AACTTGTTTAGTTGCATAATGAATTAAAACAACATATTTTGTCTTATGTT
49265027 T
1 T
49265028 GATAGATACA
Statistics
Matches: 846, Mismatches: 35, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
440 846 1.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (440 bp):
TAAAAGAGGCGGTGTTAAAGAAATATCATGTTATTGTAGCCTAGTTGCTTGCAGGGTTTGACAAA
GTTCAAATTAAATAGCTCCCGAAAAGTGACAACACATGTGCTAATGCTTTGTCCAAGTTAGCATC
CTTTGTTGTCATCGAACAAAGAGGGAAAATCCTACTCGAGCATAAAGAGACCCCGAGTTATGACA
CACTGTAAGTACTATGTATAGATCAAGAAGAAACCTAGATGAATCCAATAGTTTACACTCTCCAA
GGTGAACAAGATAACCAAGACAAGAAGGAGCTCACGAGGCTACAACTCAAAACTGCGAGGTATGT
CATTATAACAAATTACAAATACCTGTATAACTCCTAATGCGTGAATTGAATATTTGAATGTTGCA
AACTTGTTTAGTTGCATAATGAATTAAAACAACATATTTTGTCTTATGTT
Found at i:49268081 original size:18 final size:19
Alignment explanation
Indices: 49268053--49268089 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
49268043 GTTGATTATG
*
49268053 CTTTCATTTCTTTATCTTT
1 CTTTCATTTCTTAATCTTT
49268072 CTTT-ATTTCTTAATCTTT
1 CTTTCATTTCTTAATCTTT
49268090 GTATTTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.14, C:0.19, G:0.00, T:0.68
Consensus pattern (19 bp):
CTTTCATTTCTTAATCTTT
Found at i:49272141 original size:35 final size:35
Alignment explanation
Indices: 49272091--49272169 Score: 133
Period size: 35 Copynumber: 2.3 Consensus size: 35
49272081 GCTAATAGAG
49272091 TGTG-ATTTCCCTCATATGTATTATGATAGGGATT
1 TGTGCATTTCCCTCATATGTATTATGATAGGGATT
*
49272125 TTTGCATTTCCCTCATATGTATTATGATAGGGATT
1 TGTGCATTTCCCTCATATGTATTATGATAGGGATT
*
49272160 TGTGCCTTTC
1 TGTGCATTTC
49272170 TCACATCGAG
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
34 3 0.07
35 38 0.93
ACGTcount: A:0.20, C:0.15, G:0.19, T:0.46
Consensus pattern (35 bp):
TGTGCATTTCCCTCATATGTATTATGATAGGGATT
Found at i:49272400 original size:52 final size:50
Alignment explanation
Indices: 49272305--49272402 Score: 135
Period size: 52 Copynumber: 1.9 Consensus size: 50
49272295 TATCATCCCT
*
49272305 ATTTTACCCCTAGTAAAATTTGATGATTTTACCCCTAGTAAAATTTGATG
1 ATTTTACCCCTAGTAAAATTTGATAATTTTACCCCTAGTAAAATTTGATG
* *
49272355 ATTTTACCCCT-GATAAAATTTTTGATAATTTTATCCCTGGTAAAATTT
1 ATTTTACCCCTAG-TAAAA--TTTGATAATTTTACCCCTAGTAAAATTT
49272403 TGAGAATATA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
49 1 0.02
50 16 0.38
52 25 0.60
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.43
Consensus pattern (50 bp):
ATTTTACCCCTAGTAAAATTTGATAATTTTACCCCTAGTAAAATTTGATG
Found at i:49272403 original size:27 final size:25
Alignment explanation
Indices: 49272305--49272402 Score: 135
Period size: 25 Copynumber: 3.8 Consensus size: 25
49272295 TATCATCCCT
49272305 ATTTTACCCCTAGTAAAATTTGATG
1 ATTTTACCCCTAGTAAAATTTGATG
49272330 ATTTTACCCCTAGTAAAATTTGATG
1 ATTTTACCCCTAGTAAAATTTGATG
*
49272355 ATTTTACCCCT-GATAAAATTTTTGATA
1 ATTTTACCCCTAG-TAAAA--TTTGATG
* *
49272382 ATTTTATCCCTGGTAAAATTT
1 ATTTTACCCCTAGTAAAATTT
49272403 TGAGAATATA
Statistics
Matches: 67, Mismatches: 2, Indels: 8
0.87 0.03 0.10
Matches are distributed among these distances:
24 1 0.01
25 44 0.66
27 21 0.31
28 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.43
Consensus pattern (25 bp):
ATTTTACCCCTAGTAAAATTTGATG
Found at i:49275325 original size:2 final size:2
Alignment explanation
Indices: 49275318--49275351 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
49275308 CTTGAAATGA
49275318 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
49275352 GCTTATTGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49275521 original size:44 final size:45
Alignment explanation
Indices: 49275404--49275528 Score: 180
Period size: 45 Copynumber: 2.8 Consensus size: 45
49275394 AGGCGGAAGA
** *
49275404 ATTGGTGGCTTCGTCCACAACCTACATGTCAGCTTGTCTGCGAAT
1 ATTGGTGGCTTTATCCACAACCTACATGGCAGCTTGTCTGCGAAT
*
49275449 ATTGGTGGCTTTATCCACAACATACATGGCAGCTTGTCTGCGAAT
1 ATTGGTGGCTTTATCCACAACCTACATGGCAGCTTGTCTGCGAAT
* * *
49275494 ATTGGTGG-TTTATCCATAACCTGCATGGTAGCTTG
1 ATTGGTGGCTTTATCCACAACCTACATGGCAGCTTG
49275529 CCTGTAAATT
Statistics
Matches: 72, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
44 23 0.32
45 49 0.68
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.33
Consensus pattern (45 bp):
ATTGGTGGCTTTATCCACAACCTACATGGCAGCTTGTCTGCGAAT
Found at i:49276690 original size:484 final size:484
Alignment explanation
Indices: 49275777--49276753 Score: 1686
Period size: 484 Copynumber: 2.0 Consensus size: 484
49275767 CTCACCGTCT
49275777 TTAGTTTTTTGATTTTATAGATAACCCCGAGGTTAGGATTCGATAACAACATTTGGAGGAGTTTC
1 TTAG-TTTTTGATTTTATAGATAACCCCGAGGTTAGGATTCGATAACAACATTTGGAGGAGTTTC
* *
49275842 TCGAAATTCTTTTTAAATTAAAGTAATTAAAGTTTATCTTAATATTTTTTATTTTGGGATTGTAG
65 TCGAAATTCTTTTTAAATTAAAGTAATTAAAGTTTATCTTAATATTTTTAATTTTGGGATTGTAA
* *
49275907 TAAGTTTGAATATGCACTGTGGCATGAGACTTTACTTTGGGGATTTTTCATTCTGATATGCAAGA
130 TAAGTTTGAATATGCACTATGGCATAAGACTTTACTTTGGGGATTTTTCATTCTGATATGCAAGA
*
49275972 GTTGATTGCATGACATTAAGTTTTAAAAACTGCATAAATTAGTATTTGATAAGAATACACATGAA
195 GTTGATTGCATGACATTAAGTTTTAAAAACTCCATAAATTAGTATTTGATAAGAATACACATGAA
49276037 ACTTGGTTTCTATTAAAACTTGACAAAATCACTATTTTCCGCTTCGACAATGGAAATAAGTTTTA
260 ACTTGGTTTCTATTAAAACTTGACAAAATCACTATTTTCCGCTTCGACAATGGAAATAAGTTTTA
* * * *
49276102 GACGAAAATATGACTTGATTTTTGAGGTTTTAAATTGTCTGTTGATGTTTTATCGAATTTACATG
325 GACAAAAATATGACTTGATTTTTGAGGTTTTAAAATGTCTATTGATGTTTTACCGAATTTACATG
* *
49276167 AAATATTGATTTTTAACAAAATATGGTTTTAGTAAAAATTTTCGTTGTGGTTCTTATCTGCAATT
390 AAATATTGATTTTTAACAAAATATGGTTCTAGGAAAAATTTTCGTTGTGGTTCTTATCTGCAATT
49276232 CTAAGAAACAAG-TTTTAATAAAATTAGAC
455 CTAAGAAACAAGTTTTTAATAAAATTAGAC
** *
49276261 TTAGATTTTTGATTTTATAGATAACCTTGAGGTTAGGATTCGATGACAACATTTGGAGGAGTTTC
1 TTAG-TTTTTGATTTTATAGATAACCCCGAGGTTAGGATTCGATAACAACATTTGGAGGAGTTTC
* *
49276326 TCGGAATTCTTTTTAAATTAAAGTAATTAAAGTTTATCTTAATATTTTTAATTTTTGGATTGTAA
65 TCGAAATTCTTTTTAAATTAAAGTAATTAAAGTTTATCTTAATATTTTTAATTTTGGGATTGTAA
* **
49276391 TAAGTTTGAGTATGGGCTATGGCATAAGACTTTACTTTGGGGATTTTTCATTCTGATATGCAAGA
130 TAAGTTTGAATATGCACTATGGCATAAGACTTTACTTTGGGGATTTTTCATTCTGATATGCAAGA
* * * *
49276456 GTTGATTGCTTGATATTAAGTTTTAAAAACTCCATAAATTAGTGTTTGATAAGAATACGCATGAA
195 GTTGATTGCATGACATTAAGTTTTAAAAACTCCATAAATTAGTATTTGATAAGAATACACATGAA
* *
49276521 ACTTGGTTTCTATTAAAACTTGACAAAATCACTATTTTCCGCTTCGACAATGGAAATGAGTTTTT
260 ACTTGGTTTCTATTAAAACTTGACAAAATCACTATTTTCCGCTTCGACAATGGAAATAAGTTTTA
49276586 GACAAAAATATGACTTGATTTTTGAGGTTTTAAAATGTCTATTGATGTTTTACCGAATTTACATG
325 GACAAAAATATGACTTGATTTTTGAGGTTTTAAAATGTCTATTGATGTTTTACCGAATTTACATG
* *
49276651 AAATATTGATTTTTAACAGAATATGGTTCTAGGAAAAATTTTTGTTGTGGTTCTTATCTGCAATT
390 AAATATTGATTTTTAACAAAATATGGTTCTAGGAAAAATTTTCGTTGTGGTTCTTATCTGCAATT
49276716 CTAAGAAACAAGTTTTTAATAAAATTAGAC
455 CTAAGAAACAAGTTTTTAATAAAATTAGAC
49276746 TTAGTTTT
1 TTAGTTTT
49276754 CAAAATTACT
Statistics
Matches: 464, Mismatches: 28, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
484 443 0.95
485 21 0.05
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (484 bp):
TTAGTTTTTGATTTTATAGATAACCCCGAGGTTAGGATTCGATAACAACATTTGGAGGAGTTTCT
CGAAATTCTTTTTAAATTAAAGTAATTAAAGTTTATCTTAATATTTTTAATTTTGGGATTGTAAT
AAGTTTGAATATGCACTATGGCATAAGACTTTACTTTGGGGATTTTTCATTCTGATATGCAAGAG
TTGATTGCATGACATTAAGTTTTAAAAACTCCATAAATTAGTATTTGATAAGAATACACATGAAA
CTTGGTTTCTATTAAAACTTGACAAAATCACTATTTTCCGCTTCGACAATGGAAATAAGTTTTAG
ACAAAAATATGACTTGATTTTTGAGGTTTTAAAATGTCTATTGATGTTTTACCGAATTTACATGA
AATATTGATTTTTAACAAAATATGGTTCTAGGAAAAATTTTCGTTGTGGTTCTTATCTGCAATTC
TAAGAAACAAGTTTTTAATAAAATTAGAC
Found at i:49277069 original size:78 final size:78
Alignment explanation
Indices: 49276940--49277097 Score: 316
Period size: 78 Copynumber: 2.0 Consensus size: 78
49276930 TATTTGAATC
49276940 ATTGATTTCTATAATTCTCATATTTTTGTGAGATTAAGTTAAATATTTGATTTCATTAGTTTTGA
1 ATTGATTTCTATAATTCTCATATTTTTGTGAGATTAAGTTAAATATTTGATTTCATTAGTTTTGA
49277005 ATGATTTACACAA
66 ATGATTTACACAA
49277018 ATTGATTTCTATAATTCTCATATTTTTGTGAGATTAAGTTAAATATTTGATTTCATTAGTTTTGA
1 ATTGATTTCTATAATTCTCATATTTTTGTGAGATTAAGTTAAATATTTGATTTCATTAGTTTTGA
49277083 ATGATTTACACAA
66 ATGATTTACACAA
49277096 AT
1 AT
49277098 GGTTTAAAAA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 80 1.00
ACGTcount: A:0.32, C:0.08, G:0.11, T:0.49
Consensus pattern (78 bp):
ATTGATTTCTATAATTCTCATATTTTTGTGAGATTAAGTTAAATATTTGATTTCATTAGTTTTGA
ATGATTTACACAA
Found at i:49280733 original size:43 final size:42
Alignment explanation
Indices: 49280665--49280783 Score: 127
Period size: 42 Copynumber: 2.8 Consensus size: 42
49280655 AAGCTCGTAT
* * *
49280665 GATGCCAACGTCCCAGAC-GTGGTCTTACATGTAATCA-ACTATC
1 GATGCCAATGTCCTAGACAG-GGTCTTACACGTAATCATA-TA-C
**
49280708 GATG-CAACTGTCCTAGACAGGGTCTTACACAAAATCATATAC
1 GATGCCAA-TGTCCTAGACAGGGTCTTACACGTAATCATATAC
*
49280750 GATGCCAATGTCCTAGACATGGTCTTACACGTAA
1 GATGCCAATGTCCTAGACAGGGTCTTACACGTAA
49280784 ATCTCAAATC
Statistics
Matches: 64, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
42 31 0.48
43 31 0.48
44 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (42 bp):
GATGCCAATGTCCTAGACAGGGTCTTACACGTAATCATATAC
Found at i:49283162 original size:19 final size:19
Alignment explanation
Indices: 49283138--49283174 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
49283128 TTACTTTCTA
49283138 TTTTT-GTTGATTTTCTTGC
1 TTTTTGGTTG-TTTTCTTGC
49283157 TTTTTGGTTGTTTTCTTG
1 TTTTTGGTTGTTTTCTTG
49283175 TATGGTGACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.03, C:0.08, G:0.19, T:0.70
Consensus pattern (19 bp):
TTTTTGGTTGTTTTCTTGC
Found at i:49284768 original size:17 final size:18
Alignment explanation
Indices: 49284736--49284771 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
49284726 TTTGGTTATA
49284736 TTTAATTTTCGATATGTT
1 TTTAATTTTCGATATGTT
*
49284754 TTTAGTTTT-GATATGTT
1 TTTAATTTTCGATATGTT
49284771 T
1 T
49284772 CATTTAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.19, C:0.03, G:0.14, T:0.64
Consensus pattern (18 bp):
TTTAATTTTCGATATGTT
Found at i:49284902 original size:47 final size:47
Alignment explanation
Indices: 49284833--49284924 Score: 166
Period size: 47 Copynumber: 2.0 Consensus size: 47
49284823 TTTGGTCTTC
* *
49284833 AAACAATGTTTTATATTACTTATATTGTTTGATTAAAAATTATAACT
1 AAACAATGTTTCATATTACTTATATTATTTGATTAAAAATTATAACT
49284880 AAACAATGTTTCATATTACTTATATTATTTGATTAAAAATTATAA
1 AAACAATGTTTCATATTACTTATATTATTTGATTAAAAATTATAA
49284925 TTAACATTAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (47 bp):
AAACAATGTTTCATATTACTTATATTATTTGATTAAAAATTATAACT
Found at i:49284938 original size:21 final size:21
Alignment explanation
Indices: 49284914--49284964 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
49284904 TTATTTGATT
*
49284914 AAAAATTATAATTAACATTAC
1 AAAAATTATAATTAACATCAC
49284935 AAAAATTATAATTAACATCAC
1 AAAAATTATAATTAACATCAC
49284956 AAAAATTAT
1 AAAAATTAT
49284965 CTCAATAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.31
Consensus pattern (21 bp):
AAAAATTATAATTAACATCAC
Done.