Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr3
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: 26558743
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1281270 characters in sequence are not A, C, G, or T
File 58 of 79
Found at i:19226461 original size:18 final size:18
Alignment explanation
Indices: 19226435--19226469 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19226425 TACATCTACG
*
19226435 AAAATAAAAAAAAAAGAA
1 AAAAGAAAAAAAAAAGAA
*
19226453 AAAAGAAAAGAAAAAGA
1 AAAAGAAAAAAAAAAGA
19226470 CTTTGATTTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (18 bp):
AAAAGAAAAAAAAAAGAA
Found at i:19227339 original size:14 final size:14
Alignment explanation
Indices: 19227303--19227340 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
19227293 TATGATTCCC
19227303 TTTTTA-TATTTTA
1 TTTTTATTATTTTA
19227316 TTTATT-TTATTTTA
1 TTT-TTATTATTTTA
19227330 TTTTTATTATT
1 TTTTTATTATT
19227341 CATATTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTATTATTTTA
Found at i:19230929 original size:2 final size:2
Alignment explanation
Indices: 19230922--19231746 Score: 1641
Period size: 2 Copynumber: 412.5 Consensus size: 2
19230912 TCTTTCCATT
*
19230922 TC TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
19230964 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
19231006 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
19231048 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
19231090 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
19231132 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
19231174 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
19231216 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
19231258 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
19231300 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
19231342 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
19231384 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
19231426 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
19231468 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
19231510 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
19231552 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
19231594 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
19231636 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
19231678 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
19231720 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
19231747 TATTATCAAT
Statistics
Matches: 821, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 821 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:19233080 original size:10 final size:10
Alignment explanation
Indices: 19233054--19233085 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
19233044 TATTCATATA
19233054 TATATTTTAT
1 TATATTTTAT
19233064 GTATATTTTAT
1 -TATATTTTAT
19233075 TATATTTTAT
1 TATATTTTAT
19233085 T
1 T
19233086 TTCATAGCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.52
11 10 0.48
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (10 bp):
TATATTTTAT
Found at i:19237781 original size:19 final size:19
Alignment explanation
Indices: 19237757--19237829 Score: 62
Period size: 19 Copynumber: 3.9 Consensus size: 19
19237747 GATTCAATGC
19237757 AAAAAAAAACACAAAAACA
1 AAAAAAAAACACAAAAACA
** *
19237776 AAAAAAAAATGCAAAAAGA
1 AAAAAAAAACACAAAAACA
* *
19237795 AGAACAAAAA-ATAAAAAC-
1 A-AAAAAAAACACAAAAACA
*
19237813 AAAAAGAAACA-AAAAAC
1 AAAAAAAAACACAAAAAC
19237830 CTCCACCGGG
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
17 12 0.28
18 2 0.05
19 22 0.51
20 7 0.16
ACGTcount: A:0.81, C:0.11, G:0.05, T:0.03
Consensus pattern (19 bp):
AAAAAAAAACACAAAAACA
Found at i:19237790 original size:31 final size:31
Alignment explanation
Indices: 19237752--19237829 Score: 90
Period size: 31 Copynumber: 2.5 Consensus size: 31
19237742 GTGCAGATTC
19237752 AATGCAAAAAAAAACACAAAAACAAAAA-AAA
1 AATGCAAAAAAAAACA-AAAAACAAAAACAAA
*
19237783 AATGCAAAAAGAAGAACAAAAAATAAAAACAAA
1 AATGCAAAAA-AA-AACAAAAAACAAAAACAAA
19237816 AA-G-AAACAAAAAAC
1 AATGCAAA-AAAAAAC
19237830 CTCCACCGGG
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
30 3 0.07
31 15 0.36
32 15 0.36
33 9 0.21
ACGTcount: A:0.78, C:0.12, G:0.06, T:0.04
Consensus pattern (31 bp):
AATGCAAAAAAAAACAAAAAACAAAAACAAA
Found at i:19237802 original size:25 final size:23
Alignment explanation
Indices: 19237771--19237828 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 23
19237761 AAAAACACAA
*
19237771 AAACAAAAAA-AAAATGCAAAAAG
1 AAACAAAAAATAAAA-ACAAAAAG
19237794 AAGAACAAAAAATAAAAACAAAAAG
1 -A-AACAAAAAATAAAAACAAAAAG
19237819 AAACAAAAAA
1 AAACAAAAAA
19237829 CCTCCACCGG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
23 9 0.29
24 2 0.06
25 16 0.52
26 4 0.13
ACGTcount: A:0.81, C:0.09, G:0.07, T:0.03
Consensus pattern (23 bp):
AAACAAAAAATAAAAACAAAAAG
Found at i:19237817 original size:13 final size:12
Alignment explanation
Indices: 19237769--19237817 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 12
19237759 AAAAAAACAC
19237769 AAAAACAAAAAA
1 AAAAACAAAAAA
* *
19237781 AAAATGCAAAAAG
1 AAAA-ACAAAAAA
*
19237794 AAGAACAAAAAA
1 AAAAACAAAAAA
19237806 TAAAAACAAAAA
1 -AAAAACAAAAA
19237818 GAAACAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
12 10 0.34
13 19 0.66
ACGTcount: A:0.82, C:0.08, G:0.06, T:0.04
Consensus pattern (12 bp):
AAAAACAAAAAA
Found at i:19238374 original size:15 final size:14
Alignment explanation
Indices: 19238342--19238379 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
19238332 AAAAAGATGT
*
19238342 GAAAAAT-GAAAAT
1 GAAAAATGGAAAAA
19238355 GAAAAATGGAAAAA
1 GAAAAATGGAAAAA
19238369 GTAAAAATGGA
1 G-AAAAATGGA
19238380 GAGGCTAAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 7 0.32
14 6 0.27
15 9 0.41
ACGTcount: A:0.66, C:0.00, G:0.21, T:0.13
Consensus pattern (14 bp):
GAAAAATGGAAAAA
Found at i:19238375 original size:22 final size:23
Alignment explanation
Indices: 19238333--19238377 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
19238323 AAGAGAGGGA
*
19238333 AAAAGATGTGAAAAATGAAAATG
1 AAAAGATGTGAAAAATAAAAATG
19238356 AAAA-ATG-GAAAAAGTAAAAATG
1 AAAAGATGTGAAAAA-TAAAAATG
19238378 GAGAGGCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 6 0.30
22 10 0.50
23 4 0.20
ACGTcount: A:0.64, C:0.00, G:0.20, T:0.16
Consensus pattern (23 bp):
AAAAGATGTGAAAAATAAAAATG
Found at i:19239717 original size:45 final size:45
Alignment explanation
Indices: 19239666--19239805 Score: 122
Period size: 45 Copynumber: 3.2 Consensus size: 45
19239656 GGAGCGGGTT
*
19239666 GAAGATAGCAGATCTTGTCTTCCTGTATTGACAGAGAAGCAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTACTGACAGAGAAGCAGATC
* * * * ** * * * * * *
19239711 GAAGATACCAG-CCTTTTCTCCCTGGGCAG-TAGTGGAGCAGGTT
1 GAAGATAGCAGATCTTGTCTTCCTGTACTGACAGAGAAGCAGATC
* * *
19239754 GAAAATAGCAAATCTTGCCTTCCTGTACTGACAGAGAAGCAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTACTGACAGAGAAGCAGATC
19239799 GAAGATA
1 GAAGATA
19239806 CCTGCCTTAT
Statistics
Matches: 64, Mismatches: 29, Indels: 4
0.66 0.30 0.04
Matches are distributed among these distances:
43 17 0.27
44 22 0.34
45 25 0.39
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (45 bp):
GAAGATAGCAGATCTTGTCTTCCTGTACTGACAGAGAAGCAGATC
Found at i:19239844 original size:88 final size:88
Alignment explanation
Indices: 19239634--19239837 Score: 336
Period size: 88 Copynumber: 2.3 Consensus size: 88
19239624 GAAACTTTAA
* * * * * *
19239634 CCTTGTCTCCCTGGGCAGTAGTGGAGCGGGTTGAAGATAGCAGATCTTGTCTTCCTGTATTGACA
1 CCTTATCTCCCTGGGCAGTAGTGGAGCAGGTTGAAAATAGCAAATCTTGCCTTCCTGTACTGACA
19239699 GAGAAGCAGATCGAAGATACCAG
66 GAGAAGCAGATCGAAGATACCAG
*
19239722 CCTTTTCTCCCTGGGCAGTAGTGGAGCAGGTTGAAAATAGCAAATCTTGCCTTCCTGTACTGACA
1 CCTTATCTCCCTGGGCAGTAGTGGAGCAGGTTGAAAATAGCAAATCTTGCCTTCCTGTACTGACA
*
19239787 GAGAAGCAGATCGAAGATACCTG
66 GAGAAGCAGATCGAAGATACCAG
19239810 CCTTATCTCCCTGGGCAGTAGTGGAGCA
1 CCTTATCTCCCTGGGCAGTAGTGGAGCA
19239838 AATTGAAGTC
Statistics
Matches: 108, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 108 1.00
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (88 bp):
CCTTATCTCCCTGGGCAGTAGTGGAGCAGGTTGAAAATAGCAAATCTTGCCTTCCTGTACTGACA
GAGAAGCAGATCGAAGATACCAG
Found at i:19239965 original size:100 final size:100
Alignment explanation
Indices: 19239829--19240545 Score: 1114
Period size: 100 Copynumber: 7.2 Consensus size: 100
19239819 CCTGGGCAGT
* * *
19239829 AGTGGAGCAAATTGAAGTCACAACGGTAGATCTGGTTTTCCCGACAGCGCAATTAAAAAGATTGA
1 AGTGGAGCAGATTGAAGTCACAACGGCAGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGA
*
19239894 AGCCACGACGGCAGATCTTACTTCCCTGGCGGTGC
66 AGCCACAACGGCAGATCTTACTTCCCTGGCGGTGC
* * * *
19239929 AGTAGAGCAGATTGAAGCCACAACGGCAGATCTGGTTTCCCCGATAGCGCAATTAAAAATATTGA
1 AGTGGAGCAGATTGAAGTCACAACGGCAGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGA
* *
19239994 AGCCACAACGGCAGATCTTACTTCTCTGGCGGTGT
66 AGCCACAACGGCAGATCTTACTTCCCTGGCGGTGC
* *
19240029 AGTGGAGCAGATTGAAGTCACAACGGCAGATCTGGTTTCCCCGATAGCTCAATTAAAAAGATTGA
1 AGTGGAGCAGATTGAAGTCACAACGGCAGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGA
** * *
19240094 AGCCACAACGAAAGATCTTACTTCTCTGGCAGTGC
66 AGCCACAACGGCAGATCTTACTTCCCTGGCGGTGC
* * *
19240129 AGTGGAGCAGATTGAAGTCACAACGGCAGGTCTGGTATCCCCGACAGCGCATTTAAAAAGATTGA
1 AGTGGAGCAGATTGAAGTCACAACGGCAGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGA
19240194 AGCCACAACGGCAGATCTTACTTCCCTGGCGGTGC
66 AGCCACAACGGCAGATCTTACTTCCCTGGCGGTGC
19240229 AGTGGAGCAGATTGAAGTCACAACGGCAGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGA
1 AGTGGAGCAGATTGAAGTCACAACGGCAGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGA
* * *
19240294 AGCCACAACGACA-AACATTACTTCCTTGGCGGTGC
66 AGCCACAACGGCAGATC-TTACTTCCCTGGCGGTGC
* *
19240329 AGTGGAGCAAATTGAAGTCACAACTGCAGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGA
1 AGTGGAGCAGATTGAAGTCACAACGGCAGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGA
* * * *
19240394 AGCTATAACGGCAGATCTTACTTCTCTGGCGGTGT
66 AGCCACAACGGCAGATCTTACTTCCCTGGCGGTGC
19240429 AGTGGAGCAGATTGAAGTCACAACGGCAGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGA
1 AGTGGAGCAGATTGAAGTCACAACGGCAGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGA
* * *
19240494 AGCCACAACGGCAAATCTTACTTCCCTAGTGGTGC
66 AGCCACAACGGCAGATCTTACTTCCCTGGCGGTGC
*
19240529 AGCT-GAACAGATTGAAG
1 AG-TGGAGCAGATTGAAG
19240546 CTACGACAGC
Statistics
Matches: 562, Mismatches: 52, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
99 2 0.00
100 557 0.99
101 3 0.01
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.22
Consensus pattern (100 bp):
AGTGGAGCAGATTGAAGTCACAACGGCAGATCTGGTTTCCCCGACAGCGCAATTAAAAAGATTGA
AGCCACAACGGCAGATCTTACTTCCCTGGCGGTGC
Found at i:19245230 original size:20 final size:20
Alignment explanation
Indices: 19245189--19245242 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
19245179 AATTAGATTT
* **
19245189 ATTTAAAATAAAAATATTAA
1 ATTTAAATTAAAAATAGAAA
19245209 ATTTAAATTAAAAATAGAAA
1 ATTTAAATTAAAAATAGAAA
19245229 ATTATAATATTAAA
1 ATT-TAA-ATTAAA
19245243 TATTTAAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 20 0.69
21 3 0.10
22 6 0.21
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (20 bp):
ATTTAAATTAAAAATAGAAA
Found at i:19245314 original size:20 final size:20
Alignment explanation
Indices: 19245291--19245329 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
19245281 CATTGATCGG
* *
19245291 TGTTTATCAGCGTTGACCAA
1 TGTTTATAAGCATTGACCAA
19245311 TGTTTATAAGCATTGACCA
1 TGTTTATAAGCATTGACCA
19245330 GACGTTGACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (20 bp):
TGTTTATAAGCATTGACCAA
Found at i:19252335 original size:17 final size:18
Alignment explanation
Indices: 19252303--19252337 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
19252293 GATTTTAAAT
*
19252303 TAATTTTTATTATTAATA
1 TAATTTCTATTATTAATA
19252321 TAATTTCTA-TATTAATA
1 TAATTTCTATTATTAATA
19252338 GAAAGAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
TAATTTCTATTATTAATA
Found at i:19253872 original size:28 final size:29
Alignment explanation
Indices: 19253816--19253874 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
19253806 TTTCTTGTTA
*
19253816 ATTTTGGATTTATTAAATGGTGTACTTTT
1 ATTTTGGATTTATTAAATGGAGTACTTTT
19253845 ATTTGTGGACTTTATT-AAT-GAGTA-TTTT
1 ATTT-TGGA-TTTATTAAATGGAGTACTTTT
19253873 AT
1 AT
19253875 ATAATTATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
28 6 0.22
29 8 0.30
30 7 0.26
31 6 0.22
ACGTcount: A:0.25, C:0.03, G:0.17, T:0.54
Consensus pattern (29 bp):
ATTTTGGATTTATTAAATGGAGTACTTTT
Found at i:19257901 original size:126 final size:125
Alignment explanation
Indices: 19257677--19258055 Score: 564
Period size: 125 Copynumber: 3.0 Consensus size: 125
19257667 TAAGGGTTTT
*** * **
19257677 TAGGTC-CTGGAAGAAATAATTTTGAGTTGACGATTCTGATAAAATAGTATAAAATCGCTTCTAG
1 TAGGTCAC-GGAAGAAATAATTTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAG
*
19257741 CAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTTCTACAG
65 CAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
19257802 TAGGTCACGGAAGAAATAATTATTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAG
1 TAGGTCACGGAAGAAATAATT-TTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAG
* * *
19257867 CAGGATGCTATTTGAGAAGAATTTATGAAATCGCGGCCTCGT-TAGCGCGCTTTTGCTACAG
65 CAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGA-CGCGCTTTTGCTACAG
* * * * *
19257928 TAGGTCATGTAAGAAATAAATTTTTTTTGACGTTTCTAAGCAAATAATATAAAATCGCTTCTAGC
1 TAGGTCACGGAAGAAATAATTTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
* *
19257993 AAGATGCTATTTCAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
66 AGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
19258053 TAG
1 TAG
19258056 CATGTTTGGG
Statistics
Matches: 230, Mismatches: 20, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
125 118 0.51
126 112 0.49
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (125 bp):
TAGGTCACGGAAGAAATAATTTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
AGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
Found at i:19261728 original size:43 final size:45
Alignment explanation
Indices: 19261650--19261735 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 45
19261640 TTTTATTACA
*
19261650 TCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAAC
1 TCAAATAAACTTCTATTTTATTACATAAAATAATATCAAAATAAC
* *
19261695 TCAAA-AAATTTCTATTTT-TTATATAAAATAATATCAAAATA
1 TCAAATAAACTTCTATTTTATTACATAAAATAATATCAAAATA
19261736 TTAAAAATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 21 0.55
44 12 0.32
45 5 0.13
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (45 bp):
TCAAATAAACTTCTATTTTATTACATAAAATAATATCAAAATAAC
Found at i:19263909 original size:94 final size:94
Alignment explanation
Indices: 19263748--19263934 Score: 329
Period size: 94 Copynumber: 2.0 Consensus size: 94
19263738 AGGAGCATGC
* *
19263748 ATATTCCGGATATTGCATTCCAATACCCGATCTTCTGACTTTTATAACAAATAATAAATTAATAA
1 ATATTCCAGATATTGCATTCCAATACCCGATCTTCAGACTTTTATAACAAATAATAAATTAATAA
* *
19263813 TTATCTAAAAATGCATAACTAATAAATTA
66 TTATCTAAAAATGCATAAATAAAAAATTA
*
19263842 ATATTCCAGATATTGCATTCCAATCCCCGATCTTCAGACTTTTATAACAAATAATAAATTAATAA
1 ATATTCCAGATATTGCATTCCAATACCCGATCTTCAGACTTTTATAACAAATAATAAATTAATAA
19263907 TTATCTAAAAATGCATAAATAAAAAATT
66 TTATCTAAAAATGCATAAATAAAAAATT
19263935 CTTAAATAAT
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
94 88 1.00
ACGTcount: A:0.44, C:0.16, G:0.06, T:0.34
Consensus pattern (94 bp):
ATATTCCAGATATTGCATTCCAATACCCGATCTTCAGACTTTTATAACAAATAATAAATTAATAA
TTATCTAAAAATGCATAAATAAAAAATTA
Found at i:19264111 original size:11 final size:11
Alignment explanation
Indices: 19264097--19264129 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
19264087 ATTTTAAAAA
19264097 AGGAAATTGAG
1 AGGAAATTGAG
19264108 AGG-AATTGAG
1 AGGAAATTGAG
19264118 AGGAAATATGAG
1 AGGAAAT-TGAG
19264130 TGAGGATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.50
11 6 0.30
12 4 0.20
ACGTcount: A:0.45, C:0.00, G:0.36, T:0.18
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:19269050 original size:107 final size:107
Alignment explanation
Indices: 19268864--19269070 Score: 405
Period size: 107 Copynumber: 1.9 Consensus size: 107
19268854 AAGCTAAGAA
19268864 GATATTTAGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTCTCTCGAAT
1 GATATTTAGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTCTCTCGAAT
19268929 TTCCAAACGCAAAACATTGCCTCGTTTTGAAAGTTTAAAAAG
66 TTCCAAACGCAAAACATTGCCTCGTTTTGAAAGTTTAAAAAG
*
19268971 GATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTCTCTCGAAT
1 GATATTTAGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTCTCTCGAAT
19269036 TTCCAAACGCAAAACATTGCCTCGTTTTGAAAGTT
66 TTCCAAACGCAAAACATTGCCTCGTTTTGAAAGTT
19269071 NNNNNNNNNN
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
107 99 1.00
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (107 bp):
GATATTTAGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTCTCTCGAAT
TTCCAAACGCAAAACATTGCCTCGTTTTGAAAGTTTAAAAAG
Found at i:19270143 original size:3 final size:3
Alignment explanation
Indices: 19270135--19270177 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
19270125 TGTACATAGC
*
19270135 AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
19270178 CGGGACTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:19270774 original size:2 final size:2
Alignment explanation
Indices: 19270769--19270802 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
19270759 TATATATTCT
* *
19270769 TA TA TA CA TA TA TA TA TA TA TA AA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19270803 CATAATAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:19274063 original size:22 final size:22
Alignment explanation
Indices: 19274038--19274080 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
19274028 TACTCAAACA
19274038 ATAACAACAAAAT-AGTAGCAAT
1 ATAACAACAAAATGA-TAGCAAT
*
19274060 ATAATAACAAAATGATAGCAA
1 ATAACAACAAAATGATAGCAA
19274081 AACAATGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.60, C:0.12, G:0.09, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATGATAGCAAT
Found at i:19274093 original size:22 final size:22
Alignment explanation
Indices: 19274046--19274124 Score: 77
Period size: 22 Copynumber: 3.6 Consensus size: 22
19274036 CAATAACAAC
* * * *
19274046 AAAATAGTAGCAATATAATAAC
1 AAAATAATAGCAAAACAATAAA
* *
19274068 AAAATGATAGCAAAACAATGAA
1 AAAATAATAGCAAAACAATAAA
* *
19274090 AAAACAATGGCAAAACAATAAA
1 AAAATAATAGCAAAACAATAAA
*
19274112 AAAATAACAGCAA
1 AAAATAATAGCAA
19274125 TTTTTTTTTC
Statistics
Matches: 44, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.65, C:0.11, G:0.10, T:0.14
Consensus pattern (22 bp):
AAAATAATAGCAAAACAATAAA
Found at i:19284557 original size:35 final size:35
Alignment explanation
Indices: 19284517--19284585 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
19284507 CCGTCCACTG
19284517 ATACATATTTTAGCATGGTATAATTTCTGTTTTGA
1 ATACATATTTTAGCATGGTATAATTTCTGTTTTGA
*
19284552 ATACATATTTTAGCATGGTATAATTTTTGTTTTG
1 ATACATATTTTAGCATGGTATAATTTCTGTTTTG
19284586 TATTTTTGTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.28, C:0.07, G:0.14, T:0.51
Consensus pattern (35 bp):
ATACATATTTTAGCATGGTATAATTTCTGTTTTGA
Found at i:19287412 original size:11 final size:11
Alignment explanation
Indices: 19287377--19287413 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
19287367 TGTTTATGAT
19287377 TATGATATGTA
1 TATGATATGTA
**
19287388 TAAAATATGTA
1 TATGATATGTA
19287399 TATGATATGTA
1 TATGATATGTA
19287410 TATG
1 TATG
19287414 TGTGGGGTGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.43
Consensus pattern (11 bp):
TATGATATGTA
Found at i:19291424 original size:21 final size:20
Alignment explanation
Indices: 19291391--19291432 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
19291381 CCCGAAGAAC
*
19291391 TTTATTTAAAAATTGAATACT
1 TTTATTTAAAAA-TAAATACT
19291412 TTTATTGT-AAAATAAATACT
1 TTTATT-TAAAAATAAATACT
19291432 T
1 T
19291433 GGCTATCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 8 0.42
21 10 0.53
22 1 0.05
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (20 bp):
TTTATTTAAAAATAAATACT
Found at i:19291897 original size:3 final size:3
Alignment explanation
Indices: 19291891--19291935 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
19291881 AAAAAAGCTT
19291891 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
19291936 GTATACAACT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:19292090 original size:25 final size:24
Alignment explanation
Indices: 19292050--19292096 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
19292040 ATAGAAATAT
* *
19292050 ATAAAAAGAATTTTAAATTATAAC
1 ATAAAAAAAATTTTAAAATATAAC
19292074 ATAAAATAAAATTTTAAAATATA
1 ATAAAA-AAAATTTTAAAATATA
19292097 TACAAATTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (24 bp):
ATAAAAAAAATTTTAAAATATAAC
Found at i:19293714 original size:41 final size:41
Alignment explanation
Indices: 19293657--19293741 Score: 125
Period size: 41 Copynumber: 2.1 Consensus size: 41
19293647 TTTAACATAT
* * *
19293657 TCACCGGCATTTAGCCTGCTAAGCTTATAGCCTGATTCAGA
1 TCACCGACACTTAGCCTGCTAAGCTTATAACCTGATTCAGA
* *
19293698 TCACCGACACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGACACTTAGCCTGCTAAGCTTATAACCTGATTCAGA
19293739 TCA
1 TCA
19293742 NNNNNNNNNN
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (41 bp):
TCACCGACACTTAGCCTGCTAAGCTTATAACCTGATTCAGA
Found at i:19300738 original size:41 final size:41
Alignment explanation
Indices: 19300683--19300832 Score: 219
Period size: 41 Copynumber: 3.7 Consensus size: 41
19300673 TTTAACATAT
* * * *
19300683 TCACCGGCATTTAGCTTGCTAAGCTTATAGCCTGATTTAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
* * *
19300724 TCACTGACACTTAGCCTGCTAGGTTTATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
*
19300765 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
*
19300806 TCACCGGCACTTAGCCTGCTAGACTTA
1 TCACCGGCACTTAGCCTGCTAGGCTTA
19300833 AAGTCTGAAA
Statistics
Matches: 97, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 97 1.00
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
Found at i:19301267 original size:12 final size:12
Alignment explanation
Indices: 19301239--19301271 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
19301229 AGCTCATCAA
19301239 ATATACA-ATAG
1 ATATACATATAG
*
19301250 ATATACATATAT
1 ATATACATATAG
19301262 ATATACATAT
1 ATATACATAT
19301272 TCGAACTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 7 0.35
12 13 0.65
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (12 bp):
ATATACATATAG
Found at i:19301292 original size:112 final size:112
Alignment explanation
Indices: 19301176--19301493 Score: 577
Period size: 110 Copynumber: 2.9 Consensus size: 112
19301166 CACACATGTG
*
19301176 CATATATATAACATTCATACTTAACTAATTTCAATTCATATACTTTTAATTATAGCTCATCAAAT
1 CATATATATATCATTCATACTTAACTAATTTCAATTCATATACTTTTAATTATAGCTCATCAAAT
19301241 ATACAATAGATATACATATATATATACATATTCGAACTTCATTTATT
66 ATACAATAGATATACATATATATATACATATTCGAACTTCATTTATT
19301288 CATATATATATCATTCATACTTAACTAATTTCAATTCATATACTTTTAATTATAGCTCATCAAAT
1 CATATATATATCATTCATACTTAACTAATTTCAATTCATATACTTTTAATTATAGCTCATCAAAT
19301353 ATACAATAGATATAC--ATATATATACATATTCGAACTTCATTTATT
66 ATACAATAGATATACATATATATATACATATTCGAACTTCATTTATT
*
19301398 CATATATATATCATTCATACTTAACTAATTTCAATTCATATACTTTTAAATATAGCTCATCAAAT
1 CATATATATATCATTCATACTTAACTAATTTCAATTCATATACTTTTAATTATAGCTCATCAAAT
* * *
19301463 GTACAATAGTTATACATATATATATATATAT
66 ATACAATAGATATACATATATATATACATAT
19301494 GCTGATTTAA
Statistics
Matches: 199, Mismatches: 5, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
110 107 0.54
112 92 0.46
ACGTcount: A:0.41, C:0.15, G:0.03, T:0.42
Consensus pattern (112 bp):
CATATATATATCATTCATACTTAACTAATTTCAATTCATATACTTTTAATTATAGCTCATCAAAT
ATACAATAGATATACATATATATATACATATTCGAACTTCATTTATT
Found at i:19302489 original size:13 final size:13
Alignment explanation
Indices: 19302471--19302495 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19302461 CAATCAAATG
19302471 CACACAAAATAAA
1 CACACAAAATAAA
19302484 CACACAAAATAA
1 CACACAAAATAA
19302496 TATTAAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:19305217 original size:22 final size:22
Alignment explanation
Indices: 19305187--19305229 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
19305177 ACACCAAAAC
* *
19305187 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGGCACTTTTTT
19305209 AGGCCTTTAGCGGCACTTTTT
1 AGGCCTTTAGCGGCACTTTTT
19305230 AGCGCCGCAA
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:0.12, C:0.21, G:0.26, T:0.42
Consensus pattern (22 bp):
AGGCCTTTAGCGGCACTTTTTT
Found at i:19305435 original size:43 final size:42
Alignment explanation
Indices: 19305388--19305512 Score: 135
Period size: 43 Copynumber: 2.9 Consensus size: 42
19305378 AGACTAAGAG
* *
19305388 CTTTAGCGGCGTTTTTAATAGAACCGCCGCTATAGAT-TGGTGT
1 CTTTAGCGGCGTTTTT-ATAGAAGCGCCGCTATAGATCAGG-GT
* * *
19305431 CTTTAGCGGCATTTTTGTTGAAAGCGCCGCTATAGATCAGGGT
1 CTTTAGCGGCGTTTTTATAG-AAGCGCCGCTATAGATCAGGGT
* * *
19305474 CTGTAACGGCGTTTTTTATATAAGCGCCGCTATAGATCA
1 CTTTAGCGGCG-TTTTTATAGAAGCGCCGCTATAGATCA
19305513 TGACCTTTAA
Statistics
Matches: 68, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
42 2 0.03
43 58 0.85
44 8 0.12
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (42 bp):
CTTTAGCGGCGTTTTTATAGAAGCGCCGCTATAGATCAGGGT
Found at i:19305679 original size:43 final size:44
Alignment explanation
Indices: 19305523--19305678 Score: 156
Period size: 43 Copynumber: 3.6 Consensus size: 44
19305513 TGACCTTTAA
19305523 CGGCGCTTTTCCCAAAAACGCCGC-AATAGACCCTGATCTATAG
1 CGGCGCTTTTCCCAAAAACGCCGCTAATAGACCCTGATCTATAG
*** * *
19305566 CGGTATTTTTCCCACAAACGCCG-TAATAGACCCTGATCTCTAG
1 CGGCGCTTTTCCCAAAAACGCCGCTAATAGACCCTGATCTATAG
* * *** * * *
19305609 CGGCGCTTCTGCTGCAAGCGCCACTAA-AGACCCGGATCTATAG
1 CGGCGCTTTTCCCAAAAACGCCGCTAATAGACCCTGATCTATAG
* *
19305652 CGGCGCTTTTACCAAAAACACCGCTAA
1 CGGCGCTTTTCCCAAAAACGCCGCTAA
19305679 ATTTGGCAGA
Statistics
Matches: 87, Mismatches: 24, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
43 84 0.97
44 3 0.03
ACGTcount: A:0.27, C:0.32, G:0.19, T:0.22
Consensus pattern (44 bp):
CGGCGCTTTTCCCAAAAACGCCGCTAATAGACCCTGATCTATAG
Found at i:19305797 original size:16 final size:16
Alignment explanation
Indices: 19305776--19305822 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
19305766 TAACAAATCT
19305776 ATATAATAAACAAATA
1 ATATAATAAACAAATA
*
19305792 ATATAATAAATATCAATA
1 ATATAATAAACA--AATA
19305810 A-AT-ATAAACAAAT
1 ATATAATAAACAAAT
19305823 TCGTATTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
14 3 0.11
16 17 0.63
17 2 0.07
18 5 0.19
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (16 bp):
ATATAATAAACAAATA
Found at i:19305811 original size:10 final size:9
Alignment explanation
Indices: 19305776--19305816 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
19305766 TAACAAATCT
19305776 ATATAATAA
1 ATATAATAA
*
19305785 ACA-AAT-A
1 ATATAATAA
19305792 ATATAATAA
1 ATATAATAA
19305801 ATATCAATAA
1 ATAT-AATAA
19305811 ATATAA
1 ATATAA
19305817 ACAAATTCGT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
7 3 0.11
8 6 0.22
9 9 0.33
10 9 0.33
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (9 bp):
ATATAATAA
Found at i:19306013 original size:21 final size:21
Alignment explanation
Indices: 19305984--19306076 Score: 105
Period size: 21 Copynumber: 4.4 Consensus size: 21
19305974 TTTGACGCTG
19305984 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* **
19306005 CTCTACTTCCCTCGCTTTAGC
1 CTCTGCTTCCCTCGCTGCAGC
*
19306026 CTCTGCTTCCCTTGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* * * * *
19306047 CTGTACTTCTCTAGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
19306068 CTCTGCTTC
1 CTCTGCTTC
19306077 TCTTACTGCC
Statistics
Matches: 58, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 58 1.00
ACGTcount: A:0.06, C:0.43, G:0.16, T:0.34
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:19306070 original size:42 final size:42
Alignment explanation
Indices: 19305984--19306085 Score: 123
Period size: 42 Copynumber: 2.4 Consensus size: 42
19305974 TTTGACGCTG
* * **
19305984 CTCTGCTTCCCTCGCTGCAGCCTCTACTTCCCTCGCTTTAGC
1 CTCTGCTTCCCTTGCTGCAGCCTCTACTTCCCTAGCTGCAGC
* * *
19306026 CTCTGCTTCCCTTGCTGCAGCCTGTACTTCTCTAGCTGCCGC
1 CTCTGCTTCCCTTGCTGCAGCCTCTACTTCCCTAGCTGCAGC
* *
19306068 CTCTGCTTCTCTTACTGC
1 CTCTGCTTCCCTTGCTGC
19306086 CGCATCTGCT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.07, C:0.42, G:0.16, T:0.35
Consensus pattern (42 bp):
CTCTGCTTCCCTTGCTGCAGCCTCTACTTCCCTAGCTGCAGC
Found at i:19306077 original size:21 final size:21
Alignment explanation
Indices: 19306024--19306096 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
19306014 CCTCGCTTTA
* * *
19306024 GCCTCTGCTTCCCTTGCTGCA
1 GCCTCTGCTTCTCTAGCTGCC
* *
19306045 GCCTGTACTTCTCTAGCTGCC
1 GCCTCTGCTTCTCTAGCTGCC
19306066 GCCTCTGCTTCTCTTA-CTGCC
1 GCCTCTGCTTCTC-TAGCTGCC
*
19306087 GCATCTGCTT
1 GCCTCTGCTT
19306097 TAAGCTTCTG
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
21 41 0.95
22 2 0.05
ACGTcount: A:0.07, C:0.40, G:0.18, T:0.36
Consensus pattern (21 bp):
GCCTCTGCTTCTCTAGCTGCC
Found at i:19306157 original size:66 final size:66
Alignment explanation
Indices: 19306067--19306213 Score: 172
Period size: 66 Copynumber: 2.2 Consensus size: 66
19306057 CTAGCTGCCG
* ** *
19306067 CCTCTGCTTCTCTTACTGCCGCATCTGCTTTAAGCTTCT-GCTGGAGTTCTTCATAAT-TTCGTT
1 CCTCAGCTTCTCTCGCTGCCGCATCTACTTTAAG-TTCTAGCTGGAGTTCTTCAT-ATCTTCGTT
19306130 GAA
64 GAA
* * * **
19306133 CCTCAGCTTCTCTCGCTGCTGCATCTACTTTCAGTTGTAGCTGGAGTTCTTCATATCTTTTTTGA
1 CCTCAGCTTCTCTCGCTGCCGCATCTACTTTAAGTTCTAGCTGGAGTTCTTCATATCTTCGTTGA
19306198 A
66 A
*
19306199 CCTCAACTTCTCTCG
1 CCTCAGCTTCTCTCG
19306214 ATGTTGCCTC
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
65 5 0.07
66 64 0.93
ACGTcount: A:0.15, C:0.29, G:0.16, T:0.41
Consensus pattern (66 bp):
CCTCAGCTTCTCTCGCTGCCGCATCTACTTTAAGTTCTAGCTGGAGTTCTTCATATCTTCGTTGA
A
Found at i:19306235 original size:66 final size:66
Alignment explanation
Indices: 19306106--19306236 Score: 156
Period size: 66 Copynumber: 2.0 Consensus size: 66
19306096 TTAAGCTTCT
* * * *
19306106 GCTGGAGTTCTTCATAATTTCGTTGAACCTCAGCTTCTCTCGCTGCTGCATCTACTTTCAGTTGT
1 GCTGGAGTTCTTCATAATTTCGTTGAACCTCAACTTCTCTCGATGCTGCATCCACTTTAAGTTGT
19306171 A
66 A
** * * **
19306172 GCTGGAGTTCTTCAT-ATCTTTTTTGAACCTCAACTTCTCTCGATGTTGCCTCCGTTTTAAGTTG
1 GCTGGAGTTCTTCATAAT-TTCGTTGAACCTCAACTTCTCTCGATGCTGCATCCACTTTAAGTTG
19306236 T
65 T
19306237 GTAATTTGCT
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
65 2 0.04
66 52 0.96
ACGTcount: A:0.16, C:0.24, G:0.18, T:0.42
Consensus pattern (66 bp):
GCTGGAGTTCTTCATAATTTCGTTGAACCTCAACTTCTCTCGATGCTGCATCCACTTTAAGTTGT
A
Found at i:19319110 original size:42 final size:41
Alignment explanation
Indices: 19318965--19319287 Score: 351
Period size: 41 Copynumber: 7.8 Consensus size: 41
19318955 AAGGTTAATA
* * * **
19318965 CATTCGCGGCGCTTAGA-TACAAACGCCGCTGAAGACAGGAG
1 CATTAGCGGCGCTTAGACGA-AAACGCCGCTAAAGACCCGAG
* * * * ** *
19319006 AATTAGCGGTGCATATATAAAAACGCCGCTAAAAACCCGAG
1 CATTAGCGGCGCTTAGACGAAAACGCCGCTAAAGACCCGAG
** * *
19319047 CATTAGCGGCGAATAGGCGAAAACGCCGCTATAGACCCGTAG
1 CATTAGCGGCGCTTAGACGAAAACGCCGCTAAAGACCCG-AG
*
19319089 CATTAGCGGCGCTTAGACGAAAACGCCGCTAAAGACTCGGAG
1 CATTAGCGGCGCTTAGACGAAAACGCCGCTAAAGAC-CCGAG
* * * *
19319131 CATTAGCGGCGCTTAGACGAAAGCACCACTAAAGACTCGGAG
1 CATTAGCGGCGCTTAGACGAAAACGCCGCTAAAGAC-CCGAG
* * * *
19319173 CATTAGCGGCGCTTATACGAAAACGCTGCTATAGACTCGAG
1 CATTAGCGGCGCTTAGACGAAAACGCCGCTAAAGACCCGAG
* *
19319214 CATTAGCGGCGCTTAGACAAAAACGCCGCTATAGACCCGAG
1 CATTAGCGGCGCTTAGACGAAAACGCCGCTAAAGACCCGAG
*
19319255 CATTAGCGGCGCTTAGACAAAAACGCCGCTAAA
1 CATTAGCGGCGCTTAGACGAAAACGCCGCTAAA
19319288 TGTTTAAAAA
Statistics
Matches: 239, Mismatches: 40, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
41 131 0.55
42 106 0.44
43 2 0.01
ACGTcount: A:0.33, C:0.26, G:0.25, T:0.16
Consensus pattern (41 bp):
CATTAGCGGCGCTTAGACGAAAACGCCGCTAAAGACCCGAG
Found at i:19319175 original size:84 final size:82
Alignment explanation
Indices: 19318925--19319287 Score: 363
Period size: 82 Copynumber: 4.4 Consensus size: 82
19318915 TTTTGTTACT
* * * * ** * * *
19318925 ATTAGCGGCGCTTCGGCAAAAACGCCGCTAAAG-GTTAATACATTCGCGGCGCTTAGA-TACAAA
1 ATTAGCGGCGCTTAGACGAAAACGCCGCTAAAGACTCGA-GCATTAGCGGCGCTTAGACGA-AAA
* *
19318988 CGCCGCTGA-AGACAGGAGA
64 CGCCGCT-ATAGACCGGAGC
* * * ** * * ** *
19319007 ATTAGCGGTGCATATATAAAAACGCCGCTAAAAACCCGAGCATTAGCGGCGAATAGGCGAAAACG
1 ATTAGCGGCGCTTAGACGAAAACGCCGCTAAAGACTCGAGCATTAGCGGCGCTTAGACGAAAACG
*
19319072 CCGCTATAGACCCGTAGC
66 CCGCTATAGA-CCGGAGC
*
19319090 ATTAGCGGCGCTTAGACGAAAACGCCGCTAAAGACTCGGAGCATTAGCGGCGCTTAGACGAAAGC
1 ATTAGCGGCGCTTAGACGAAAACGCCGCTAAAGACTC-GAGCATTAGCGGCGCTTAGACGAAAAC
* * *
19319155 ACCACTAAAGACTCGGAGC
65 GCCGCTATAGAC-CGGAGC
* * * *
19319174 ATTAGCGGCGCTTATACGAAAACGCTGCTATAGACTCGAGCATTAGCGGCGCTTAGACAAAAACG
1 ATTAGCGGCGCTTAGACGAAAACGCCGCTAAAGACTCGAGCATTAGCGGCGCTTAGACGAAAACG
*
19319239 CCGCTATAGACCCGAGC
66 CCGCTATAGACCGGAGC
*
19319256 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAA
1 ATTAGCGGCGCTTAGACGAAAACGCCGCTAAA
19319288 TGTTTAAAAA
Statistics
Matches: 227, Mismatches: 48, Indels: 12
0.79 0.17 0.04
Matches are distributed among these distances:
81 1 0.00
82 85 0.37
83 71 0.31
84 70 0.31
ACGTcount: A:0.33, C:0.26, G:0.25, T:0.16
Consensus pattern (82 bp):
ATTAGCGGCGCTTAGACGAAAACGCCGCTAAAGACTCGAGCATTAGCGGCGCTTAGACGAAAACG
CCGCTATAGACCGGAGC
Found at i:19319459 original size:40 final size:39
Alignment explanation
Indices: 19319336--19319462 Score: 112
Period size: 40 Copynumber: 3.2 Consensus size: 39
19319326 GGTTTTTTGT
* * *
19319336 GGCGCTTTATATAAAACGCCGTTAATTC-CTATTTTTAGC
1 GGCGCTTTA-GTAAAACGCCGCTAATGCTCTATTTTTAGC
** * **
19319375 GGCGCTTCCGTATAAACGCCGCTGATGCTCTACCTTTAGC
1 GGCGCTTTAGTA-AAACGCCGCTAATGCTCTATTTTTAGC
* * * *
19319415 GGCGCTTTGGCTAAATCGCCGCTAATGCTCTATTTTTTGT
1 GGCGCTTTAG-TAAAACGCCGCTAATGCTCTATTTTTAGC
19319455 GGCGCTTT
1 GGCGCTTT
19319463 TGTTCCAAAC
Statistics
Matches: 69, Mismatches: 16, Indels: 5
0.77 0.18 0.06
Matches are distributed among these distances:
38 2 0.03
39 19 0.28
40 46 0.67
41 2 0.03
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.35
Consensus pattern (39 bp):
GGCGCTTTAGTAAAACGCCGCTAATGCTCTATTTTTAGC
Found at i:19319603 original size:141 final size:141
Alignment explanation
Indices: 19319349--19319623 Score: 514
Period size: 141 Copynumber: 2.0 Consensus size: 141
19319339 GCTTTATATA
*
19319349 AAACGCCGTTAATTCCTATTTTTAGCGGCGCTTCCGTATAAACGCCGCTGATGCTCTACCTTTAG
1 AAACGCCGCTAATTCCTATTTTTAGCGGCGCTTCCGTATAAACGCCGCTGATGCTCTACCTTTAG
* *
19319414 CGGCGCTTTGGCTAAATCGCCGCTAATGCTCTATTTTTTGTGGCGCTTTTGTTCCAAACGCCGCA
66 CAGCACTTTGGCTAAATCGCCGCTAATGCTCTATTTTTTGTGGCGCTTTTGTTCCAAACGCCGCA
19319479 AAAAGTTCCGC
131 AAAAGTTCCGC
19319490 AAACGCCGCTAATTCCTATTTTTAGCGGCGCTTCCGTATAAACGCCGCTGATGCTCTACCTTTAG
1 AAACGCCGCTAATTCCTATTTTTAGCGGCGCTTCCGTATAAACGCCGCTGATGCTCTACCTTTAG
*
19319555 CAGCACTTTGGCTAAATCGCCGCTAATGCTCTATTTTTTGTGGTGCTTTTGTTCCAAACGCCGCA
66 CAGCACTTTGGCTAAATCGCCGCTAATGCTCTATTTTTTGTGGCGCTTTTGTTCCAAACGCCGCA
19319620 AAAA
131 AAAA
19319624 ATGCCGCTAA
Statistics
Matches: 130, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
141 130 1.00
ACGTcount: A:0.21, C:0.27, G:0.20, T:0.32
Consensus pattern (141 bp):
AAACGCCGCTAATTCCTATTTTTAGCGGCGCTTCCGTATAAACGCCGCTGATGCTCTACCTTTAG
CAGCACTTTGGCTAAATCGCCGCTAATGCTCTATTTTTTGTGGCGCTTTTGTTCCAAACGCCGCA
AAAAGTTCCGC
Found at i:19321257 original size:27 final size:27
Alignment explanation
Indices: 19321227--19321285 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
19321217 TGAAAAAGGT
19321227 GGCACCAATGGTGCCTTTCCCATAGGC
1 GGCACCAATGGTGCCTTTCCCATAGGC
* *
19321254 GGCACCAATGGTGCCTTTCTCATAGTC
1 GGCACCAATGGTGCCTTTCCCATAGGC
19321281 GGCAC
1 GGCAC
19321286 AGGACTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.19, C:0.32, G:0.25, T:0.24
Consensus pattern (27 bp):
GGCACCAATGGTGCCTTTCCCATAGGC
Found at i:19322031 original size:27 final size:27
Alignment explanation
Indices: 19321993--19322055 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
19321983 TTTTAGTCCT
*
19321993 GTGCCGCCTATGAGAAAGGCACTATTG
1 GTGCCGCCTATGAGAAAGGCACCATTG
*
19322020 GTGCCGCCTATGGGAAAGGCACCATTG
1 GTGCCGCCTATGAGAAAGGCACCATTG
19322047 GTGCCGCCT
1 GTGCCGCCT
19322056 TTTTCATGCC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.21, C:0.27, G:0.32, T:0.21
Consensus pattern (27 bp):
GTGCCGCCTATGAGAAAGGCACCATTG
Found at i:19332979 original size:26 final size:26
Alignment explanation
Indices: 19332947--19333015 Score: 122
Period size: 26 Copynumber: 2.7 Consensus size: 26
19332937 AAATAAAAAA
19332947 TTACCAAAATAT-TAAATTTTTTTTAT
1 TTACCAAAATATATAAA-TTTTTTTAT
19332973 TTACCAAAATATATAAATTTTTTTAT
1 TTACCAAAATATATAAATTTTTTTAT
19332999 TTACCAAAATATATAAA
1 TTACCAAAATATATAAA
19333016 AAACCAAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
26 38 0.90
27 4 0.10
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.46
Consensus pattern (26 bp):
TTACCAAAATATATAAATTTTTTTAT
Found at i:19333150 original size:27 final size:27
Alignment explanation
Indices: 19333073--19333151 Score: 113
Period size: 27 Copynumber: 2.9 Consensus size: 27
19333063 AACTGGTCAC
** *
19333073 GCCAATGGAATTGGCGGCACCAAAGGT
1 GCCAATGCCATTGGCGGCACCAATGGT
**
19333100 GCCAAAACCATTGGCGGCACCAATGGT
1 GCCAATGCCATTGGCGGCACCAATGGT
19333127 GCCAATGCCATTGGCGGCACCAATG
1 GCCAATGCCATTGGCGGCACCAATG
19333152 CCATACTAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.28, C:0.28, G:0.29, T:0.15
Consensus pattern (27 bp):
GCCAATGCCATTGGCGGCACCAATGGT
Found at i:19333268 original size:11 final size:11
Alignment explanation
Indices: 19333252--19333292 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
19333242 GATGCTGTGG
19333252 AAAAGAAGAGA
1 AAAAGAAGAGA
19333263 AAAAG-AGAGA
1 AAAAGAAGAGA
*
19333273 AAAAGAGGAGA
1 AAAAGAAGAGA
19333284 AAAAGAAGA
1 AAAAGAAGA
19333293 TATTTTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
10 10 0.37
11 17 0.63
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAGA
Found at i:19333353 original size:19 final size:21
Alignment explanation
Indices: 19333315--19333353 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
19333305 AATAATTGAT
*
19333315 TATATTGTTGTTATTATTTTG
1 TATATTGTTGTTAATATTTTG
19333336 TATATT-TTG-TAATATTTT
1 TATATTGTTGTTAATATTTT
19333354 TTGTTTTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (21 bp):
TATATTGTTGTTAATATTTTG
Found at i:19333415 original size:3 final size:3
Alignment explanation
Indices: 19333399--19333433 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
19333389 AAAATAATAG
*
19333399 TAT TAGT TAG TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT T
19333434 NNNNNNNNNN
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:19340901 original size:19 final size:19
Alignment explanation
Indices: 19340866--19340903 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
19340856 TTTAAACACA
19340866 CAAATATTACAAAAAAATT
1 CAAATATTACAAAAAAATT
*
19340885 CAAAT-TTATAAATAAAATT
1 CAAATATTACAAA-AAAATT
19340904 ACCTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.32
Consensus pattern (19 bp):
CAAATATTACAAAAAAATT
Found at i:19340965 original size:33 final size:32
Alignment explanation
Indices: 19340915--19341031 Score: 103
Period size: 33 Copynumber: 3.4 Consensus size: 32
19340905 CCTTTTTTTC
*
19340915 CTTTTTTTTTCCT-TCCTTTCCTCTTCTTCTT
1 CTTTTTTTTTCTTCTCCTTTCCTCTTCTTCTT
19340946 CTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTT
1 CTTTTTTTT-TCTTCTCCTTTCC---TC-TT-CTTC-TT
*
19340985 CTTTCTTTTTTCTTCTCTTTTCCT-TCTCTTCTT
1 CTTT-TTTTTTCTTCTCCTTTCCTCT-TCTTCTT
*
19341018 CTTCTTTCTTTCTT
1 CTT-TTTTTTTCTT
19341032 TTTTTCTCTT
Statistics
Matches: 72, Mismatches: 3, Indels: 20
0.76 0.03 0.21
Matches are distributed among these distances:
31 9 0.12
32 3 0.04
33 21 0.29
34 6 0.08
35 1 0.01
36 3 0.04
37 2 0.03
38 4 0.06
39 18 0.25
40 5 0.07
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (32 bp):
CTTTTTTTTTCTTCTCCTTTCCTCTTCTTCTT
Found at i:19340969 original size:38 final size:37
Alignment explanation
Indices: 19340916--19341100 Score: 152
Period size: 38 Copynumber: 4.9 Consensus size: 37
19340906 CTTTTTTTCC
19340916 TTTTTT-TT-TCC-TTCCTTTCCTCTTCTTC-TTCTTT
1 TTTTTTCTTCTCCTTTCCTTTCCT-TTCTTCTTTCTTT
*
19340950 TTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTCTTT
1 TTTTT-TCTTCTCCTTTCCTTTCCTTT-CTTCTTTCTTT
* *
19340989 CTTTTTTCTTCTCTTTTCCTTCTCTTCTTCTTCTTTCTTT
1 -TTTTTTCTTCTCCTTTCCTT-TCCT-TTCTTCTTTCTTT
* *
19341029 CTTTTT-TTCT-CTTCTCCTTTCCCTTTCTTTCCTTCTTT
1 TTTTTTCTTCTCCTT-TCCTTT-CCTTTC-TTCTTTCTTT
* * *
19341067 TTCTTTCTTC-CCTCTCCTTT-CTTCCTTTCTTTCT
1 TTTTTTCTTCTCCTTTCCTTTCCTTTC-TTCTTTCT
19341101 CTCTTTCTTC
Statistics
Matches: 124, Mismatches: 13, Indels: 26
0.76 0.08 0.16
Matches are distributed among these distances:
34 5 0.04
35 1 0.01
36 14 0.11
37 11 0.09
38 43 0.35
39 30 0.24
40 18 0.15
41 2 0.02
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (37 bp):
TTTTTTCTTCTCCTTTCCTTTCCTTTCTTCTTTCTTT
Found at i:19340973 original size:48 final size:43
Alignment explanation
Indices: 19340937--19341075 Score: 157
Period size: 44 Copynumber: 3.3 Consensus size: 43
19340927 TTCCTTTCCT
*
19340937 CTTC-TTC-TTCTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
1 CTTCTTTCTTTCTTTTTTTTCTCTTCTCCTTTCCTTTTCCTTC
* *
19340978 CTTCTTTCTTTCTTTTTTCTTCTCTTTTCC-TT-CTCTT-CTT-
1 CTTCTTTCTTTCTTTTTT-TTCTCTTCTCCTTTCCTTTTCCTTC
* *
19341018 CTTCTTTCTTTC-TTTTTTTCTCTTCTCCTTTCCCTTTCTTTC
1 CTTCTTTCTTTCTTTTTTTTCTCTTCTCCTTTCCTTTTCCTTC
19341060 CTTCTTTTTCTTTCTT
1 CTTC--TTTCTTTCTT
19341076 CCCTCTCCTT
Statistics
Matches: 81, Mismatches: 7, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
38 10 0.12
39 7 0.09
40 15 0.19
41 8 0.10
42 11 0.14
43 11 0.14
44 18 0.22
45 1 0.01
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (43 bp):
CTTCTTTCTTTCTTTTTTTTCTCTTCTCCTTTCCTTTTCCTTC
Found at i:19340986 original size:4 final size:4
Alignment explanation
Indices: 19340970--19341119 Score: 96
Period size: 4 Copynumber: 37.0 Consensus size: 4
19340960 CTCCTTTCCT
* *
19340970 TTTC TTTC CTTC TTTC TTTC TTT- TTTC TTCTC TTTTC CTTC TCTTC -TTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-TC -TTTC TTTC T-TTC TTTC
* * *
19341019 -TTC TTTC TTTC TTTT TTTC TCTTC -TCC TTTCCC TTTC TTTC CTTC -TT-
1 TTTC TTTC TTTC TTTC TTTC T-TTC TTTC TTT--C TTTC TTTC TTTC TTTC
* * * * *
19341066 TTTC TTTC TTCCC TCTCC TTTC TTCC TTTC TTTC TCTC TTTC TTCC TTTC
1 TTTC TTTC TT-TC T-TTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
19341116 TTTC
1 TTTC
19341120 CCTCCCCTTC
Statistics
Matches: 116, Mismatches: 17, Indels: 26
0.73 0.11 0.16
Matches are distributed among these distances:
3 15 0.13
4 79 0.68
5 15 0.13
6 7 0.06
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (4 bp):
TTTC
Found at i:19341006 original size:29 final size:28
Alignment explanation
Indices: 19340921--19341071 Score: 85
Period size: 26 Copynumber: 5.7 Consensus size: 28
19340911 TTTCCTTTTT
*
19340921 TTTTCCTTC-CTTTCCTCTTC-TTC-TTC
1 TTTTCCTTCTC-TTCTTCTTCTTTCTTTC
**
19340947 TTTTTTTTCTCTTC-TC--CTTTCCTTT-
1 TTTTCCTTCTCTTCTTCTTCTTT-CTTTC
* *
19340972 TCTTTCCTTCT-TTCTTTCTTTTTTCTTCTC
1 T-TTTCCTTCTCTT-CTTCTTCTTTCTT-TC
19341002 TTTTCCTTCTCTTCTTCTTCTTTCTTTC
1 TTTTCCTTCTCTTCTTCTTCTTTCTTTC
* * **
19341030 TTTT-TTTCTCTTCTCCTT-TCCCTTTC
1 TTTTCCTTCTCTTCTTCTTCTTTCTTTC
19341056 -TTTCCTTCT-TT-TTCTT
1 TTTTCCTTCTCTTCTTCTT
19341072 TCTTCCCTCT
Statistics
Matches: 98, Mismatches: 14, Indels: 28
0.70 0.10 0.20
Matches are distributed among these distances:
23 1 0.01
24 6 0.06
25 11 0.11
26 29 0.30
27 15 0.15
28 9 0.09
29 24 0.24
30 3 0.03
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (28 bp):
TTTTCCTTCTCTTCTTCTTCTTTCTTTC
Found at i:19341086 original size:20 final size:22
Alignment explanation
Indices: 19341041--19341128 Score: 84
Period size: 20 Copynumber: 4.3 Consensus size: 22
19341031 TTTTTTCTCT
*
19341041 TCTCCTTTC--CCTTTCTTTCC
1 TCTCCTTTCTTCCTTTCTTCCC
19341061 T-T-CTTT-TT-CTTTCTTCCC
1 TCTCCTTTCTTCCTTTCTTCCC
*
19341079 TCTCCTTTCTTCCTTTCTT-TC
1 TCTCCTTTCTTCCTTTCTTCCC
19341100 TCT-CTTTCTTCCTTTCTTTCCC
1 TCTCCTTTCTTCCTTTC-TTCCC
*
19341122 TCCCCTT
1 TCTCCTT
19341129 CTGTTAATTG
Statistics
Matches: 55, Mismatches: 4, Indels: 15
0.74 0.05 0.20
Matches are distributed among these distances:
18 14 0.25
19 2 0.04
20 18 0.33
21 8 0.15
22 10 0.18
23 3 0.05
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (22 bp):
TCTCCTTTCTTCCTTTCTTCCC
Found at i:19341106 original size:82 final size:84
Alignment explanation
Indices: 19340922--19341119 Score: 236
Period size: 82 Copynumber: 2.4 Consensus size: 84
19340912 TTCCTTTTTT
* *
19340922 TTTCCTTCCTTTC-CTCT-TC-TTC-TTCTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCT
1 TTTCCTTCCTTTCTTTCTCTCTTTCTTTC-TTTTTTTCTCTTCTCCTTTCCCTTTCTTTCCTTCT
* * *
19340983 TTCTTTCTTTTTTCTTCTCT
65 TTCTTTCTTTTTCCCTCTCC
19341003 TTTCCTT-CTCTTC-TTCT-TCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCCTTTCTTTCCTTC-
1 TTTCCTTCCT-TTCTTTCTCTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCCTTTCTTTCCTTCT
19341064 TT-TTTCTTTCTTCCCTCTCC
65 TTCTTTCTTT-TTCCCTCTCC
* *
19341084 TTT-CTTCCTTTCTTTCTCTCTTTCTTCCTTTCTTTC
1 TTTCCTTCCTTTCTTTCTCTCTTTCTTTCTTTTTTTC
19341120 CCTCCCCTTC
Statistics
Matches: 103, Mismatches: 7, Indels: 13
0.84 0.06 0.11
Matches are distributed among these distances:
80 15 0.15
81 33 0.32
82 52 0.50
83 3 0.03
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (84 bp):
TTTCCTTCCTTTCTTTCTCTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCCTTTCTTTCCTTCTT
TCTTTCTTTTTCCCTCTCC
Found at i:19341119 original size:70 final size:70
Alignment explanation
Indices: 19340905--19341122 Score: 180
Period size: 72 Copynumber: 3.0 Consensus size: 70
19340895 AATAAAATTA
* * *
19340905 CCTTTTTTTCCTT-TTTTTTTCCTT-CCTTTCCTCTTCTTCTTCTTT-TTTTTCTC-TTC-TCCT
1 CCTTTCTTTCCTTCTTTTTTTTCTTCCCTTTCCT-TTCTTC--CTTTCTTTCTCTCTTTCTTCCT
19340965 TTCCTTT-
63 TTCCTTTC
* * * * * * *
19340972 TCTTTCCTTCTTTCTTTCTTTTTTCTTCTCTTTTCCTTCTCTTCTTCTTCTTTCTTTCTTTTTTT
1 CCTTTCTTTCCTTC-TT-TTTTTTCTTC-CCTTTCCTT-TCTTCCT-TTCTTTCTCTC-TTTCTT
19341037 CTCTTCTCCTTTC
60 C-CTT-TCCTTTC
*
19341050 CCTTTCTTTCCTTCTTTTTCTTTCTTCCCTCTCCTTTCTTCCTTTCTTTCTCTCTTTCTTCCTTT
1 CCTTTCTTTCCTTCTTTTT-TTTCTTCCCTTTCCTTTCTTCCTTTCTTTCTCTCTTTCTTCCTTT
19341115 -CTTTC
65 CCTTTC
19341120 CCT
1 CCT
19341123 CCCCTTCTGT
Statistics
Matches: 118, Mismatches: 18, Indels: 27
0.72 0.11 0.17
Matches are distributed among these distances:
67 9 0.08
69 2 0.02
70 17 0.14
71 4 0.03
72 21 0.18
73 6 0.05
74 12 0.10
75 8 0.07
76 13 0.11
77 15 0.13
78 11 0.09
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (70 bp):
CCTTTCTTTCCTTCTTTTTTTTCTTCCCTTTCCTTTCTTCCTTTCTTTCTCTCTTTCTTCCTTTC
CTTTC
Found at i:19363096 original size:11 final size:11
Alignment explanation
Indices: 19363080--19363105 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
19363070 AATATCTAAA
19363080 ATATGATTTAT
1 ATATGATTTAT
19363091 ATATGATTTAT
1 ATATGATTTAT
19363102 ATAT
1 ATAT
19363106 TAAATTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (11 bp):
ATATGATTTAT
Found at i:19363135 original size:23 final size:24
Alignment explanation
Indices: 19363099--19363154 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 24
19363089 ATATATGATT
*
19363099 TATATATTAAATTAAATA-TTACAAA
1 TATAT-TTATATTAAATATTTA-AAA
*
19363124 TA-ATTTATATTAATTATTTAAAA
1 TATATTTATATTAAATATTTAAAA
19363147 TATATTTA
1 TATATTTA
19363155 AAATTTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 15 0.56
24 10 0.37
25 2 0.07
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
TATATTTATATTAAATATTTAAAA
Found at i:19366352 original size:72 final size:72
Alignment explanation
Indices: 19366234--19366374 Score: 230
Period size: 72 Copynumber: 2.0 Consensus size: 72
19366224 AGGAACTAAG
* *
19366234 GGAGGCAACAGAGTAAATATATTGAATGTTAAGTAAGTCCACATGAAATTTACTTAACTTACCTT
1 GGAGGCAACAGAGTAAACATATTAAATGTTAAGTAAGTCCACATGAAATTTACTTAACTTACCTT
19366299 AACAAAA
66 AACAAAA
* *
19366306 GGAGGCAACGGAGTAAACATATTAAATGCTT-AGTAAGTCCATATGAAATTTACTTAACTTACCT
1 GGAGGCAACAGAGTAAACATATTAAATG-TTAAGTAAGTCCACATGAAATTTACTTAACTTACCT
19366370 TAACA
65 TAACA
19366375 TTACAACAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
72 62 0.97
73 2 0.03
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (72 bp):
GGAGGCAACAGAGTAAACATATTAAATGTTAAGTAAGTCCACATGAAATTTACTTAACTTACCTT
AACAAAA
Found at i:19370364 original size:13 final size:13
Alignment explanation
Indices: 19370348--19370372 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19370338 TATAACCCCA
19370348 AAAAATAAAAAAT
1 AAAAATAAAAAAT
19370361 AAAAATAAAAAA
1 AAAAATAAAAAA
19370373 GAGAGAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:19372005 original size:9 final size:9
Alignment explanation
Indices: 19371991--19372018 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
19371981 GGAACAGAAT
19371991 AATAATAAA
1 AATAATAAA
19372000 AATAATAAA
1 AATAATAAA
19372009 AATAATAAA
1 AATAATAAA
19372018 A
1 A
19372019 TAGTAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AATAATAAA
Found at i:19387486 original size:31 final size:31
Alignment explanation
Indices: 19387451--19387511 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
19387441 CTTACACTCT
**
19387451 AATTTGATTCGTTTTAGTCCCTTTACTTTTC
1 AATTTGATTAATTTTAGTCCCTTTACTTTTC
* * *
19387482 AATTTGGTTAATTTTAGTCCTTTTATTTTT
1 AATTTGATTAATTTTAGTCCCTTTACTTTT
19387512 TTTAATTTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.18, C:0.13, G:0.10, T:0.59
Consensus pattern (31 bp):
AATTTGATTAATTTTAGTCCCTTTACTTTTC
Found at i:19388812 original size:2 final size:2
Alignment explanation
Indices: 19388805--19388833 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
19388795 AATCAAGGGG
19388805 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
19388834 TTGGTGATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:19390106 original size:21 final size:21
Alignment explanation
Indices: 19390077--19390116 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
19390067 ATAAGAAAAC
*
19390077 AAAACTATAACATTTTTATGA
1 AAAAATATAACATTTTTATGA
**
19390098 AAAAATATATTATTTTTAT
1 AAAAATATAACATTTTTAT
19390117 AATATATAAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (21 bp):
AAAAATATAACATTTTTATGA
Found at i:19390319 original size:29 final size:27
Alignment explanation
Indices: 19390275--19390328 Score: 63
Period size: 29 Copynumber: 1.9 Consensus size: 27
19390265 CCATTTGAAA
*
19390275 TTTTTTTTAGAATTTACATAATATACT
1 TTTTTTTTAGAATTTACAAAATATACT
* *
19390302 TTTTTTGTTATAACTTTATAAAATATA
1 TTTTTT-TTAGAA-TTTACAAAATATA
19390329 TAAATGGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 6 0.27
28 5 0.23
29 11 0.50
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.56
Consensus pattern (27 bp):
TTTTTTTTAGAATTTACAAAATATACT
Found at i:19390671 original size:34 final size:33
Alignment explanation
Indices: 19390628--19390721 Score: 116
Period size: 34 Copynumber: 2.7 Consensus size: 33
19390618 GAATTTTTTT
19390628 TAAATTTAATTAAATTAAGTTTTAGGGGTTTTAAG
1 TAAA-TTAATTAAATTAAG-TTTAGGGGTTTTAAG
* *
19390663 TAAATTAATTAAAATAAAGTTTAGGGTTTTTAAG
1 TAAATTAATT-AAATTAAGTTTAGGGGTTTTAAG
* *
19390697 AAAATTAATTAAATTAGGGTTTAGG
1 TAAATTAATTAAATTA-AGTTTAGG
19390722 TTTTAAAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
33 5 0.10
34 36 0.69
35 11 0.21
ACGTcount: A:0.41, C:0.00, G:0.17, T:0.41
Consensus pattern (33 bp):
TAAATTAATTAAATTAAGTTTAGGGGTTTTAAG
Found at i:19391055 original size:126 final size:126
Alignment explanation
Indices: 19390821--19391367 Score: 547
Period size: 126 Copynumber: 4.2 Consensus size: 126
19390811 GATTTTGTTT
* * * * * *
19390821 TCTTTTTCTACAGTAGTTTCTGAAAAATTAATTTTGAGAAGATACTTCTGAAAAGATAATGTCAA
1 TCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGATAGTTTTGAAAAAATAGTGTCAA
* * * *
19390886 ACACGCTTCAAGCAGGATGTACTGTCAGCAAAAGTACTAAAAAAAGCTCCCACGTGGACGC
66 AAACGCTTCAAACAGGATGCACTGTCAGCAAAATTACTAAAAAAAGCTCCCACGTGGACGC
* * *
19390947 TCTTTTTCTACAATAGTTCTTGAAAAAATAATTTTGAGAAGACAGTTTTGAAAAAATAGTGTCAA
1 TCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGATAGTTTTGAAAAAATAGTGTCAA
* * *
19391012 AAACGCTTCAATCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTTCCACGTGGACGC
66 AAACGCTTCAAACAGGATGCACTGTCAGCAAAATTACTAAAAAAAGCTCCCACGTGGACGC
* *
19391073 TCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGAAAAAAATAATTTAGAGAAGACGG
1 TCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAG------ATAGTTTTGA-AA-A---
* * * *
19391138 TTCTGAAAAAAATAGTGTCAAAAACGCTTCAAACAGGATACACTGTCAACAAAATTACTGAAAAA
55 -----AATA-----GTGTCAAAAACGCTTCAAACAGGATGCACTGTCAGCAAAATTACTAAAAAA
** *
19391203 AGCCTCATACAT-GACGC
110 AG-CTCCCACGTGGACGC
* * * * * * *
19391220 TATTTTTCTACAGTAGATCCTGAAAAAATAATTTAGAGAAGATGGTTATGAAGAAATAGTGTTAA
1 TCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGATAGTTTTGAAAAAATAGTGTCAA
* * * *
19391285 AAACGCTTCAAAGAGGATGCACTGTTAGCAAAATTACTAAAAAAAGCTTCCAGGTGGACGC
66 AAACGCTTCAAACAGGATGCACTGTCAGCAAAATTACTAAAAAAAGCTCCCACGTGGACGC
* *
19391346 ACTTTTTCTAAAGTAGTTCCTG
1 TCTTTTTCTACAGTAGTTCCTG
19391368 CTTGGCCTTA
Statistics
Matches: 346, Mismatches: 52, Indels: 46
0.78 0.12 0.10
Matches are distributed among these distances:
125 4 0.01
126 220 0.64
131 3 0.01
132 7 0.02
133 2 0.01
134 1 0.00
139 1 0.00
140 1 0.00
141 6 0.02
142 3 0.01
147 93 0.27
148 5 0.01
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (126 bp):
TCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGATAGTTTTGAAAAAATAGTGTCAA
AAACGCTTCAAACAGGATGCACTGTCAGCAAAATTACTAAAAAAAGCTCCCACGTGGACGC
Found at i:19391120 original size:20 final size:20
Alignment explanation
Indices: 19391095--19391134 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
19391085 GTAGTTCCTG
*
19391095 AAAAAATAATTTTGAGAAGA
1 AAAAAATAATTTAGAGAAGA
19391115 AAAAAATAATTTAGAGAAGA
1 AAAAAATAATTTAGAGAAGA
19391135 CGGTTCTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (20 bp):
AAAAAATAATTTAGAGAAGA
Found at i:19391235 original size:147 final size:146
Alignment explanation
Indices: 19390969--19391261 Score: 453
Period size: 147 Copynumber: 2.0 Consensus size: 146
19390959 ATAGTTCTTG
* * * *
19390969 AAAAAATAATTTTGAGAAGACAGTTTTGAAAAAATAGTGTCAAAAACGCTTCAATCAGGATGCAC
1 AAAAAATAATTTAGAGAAGACAGTTCTGAAAAAATAGTGTCAAAAACGCTTCAAACAGGATACAC
* * * * *
19391034 TGTCAGCAAAATTACTGAAAAAAGCTTCCACGTGGACGCTCTTTTTCTACAGTAGTTCCTGAAAA
66 TGTCAACAAAATTACTGAAAAAAGCCTCCACATGGACGCTATTTTTCTACAGTAGATCCTGAAAA
*
19391099 AATAATTTTGAGAAGA
131 AATAATTTAGAGAAGA
*
19391115 AAAAAATAATTTAGAGAAGACGGTTCTGAAAAAAATAGTGTCAAAAACGCTTCAAACAGGATACA
1 AAAAAATAATTTAGAGAAGACAGTTCTG-AAAAAATAGTGTCAAAAACGCTTCAAACAGGATACA
*
19391180 CTGTCAACAAAATTACTGAAAAAAGCCTCATACAT-GACGCTATTTTTCTACAGTAGATCCTGAA
65 CTGTCAACAAAATTACTGAAAAAAGCCTC-CACATGGACGCTATTTTTCTACAGTAGATCCTGAA
19391244 AAAATAATTTAGAGAAGA
129 AAAATAATTTAGAGAAGA
19391262 TGGTTATGAA
Statistics
Matches: 133, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
146 25 0.19
147 105 0.79
148 3 0.02
ACGTcount: A:0.43, C:0.15, G:0.16, T:0.26
Consensus pattern (146 bp):
AAAAAATAATTTAGAGAAGACAGTTCTGAAAAAATAGTGTCAAAAACGCTTCAAACAGGATACAC
TGTCAACAAAATTACTGAAAAAAGCCTCCACATGGACGCTATTTTTCTACAGTAGATCCTGAAAA
AATAATTTAGAGAAGA
Found at i:19391367 original size:273 final size:272
Alignment explanation
Indices: 19390843--19391367 Score: 719
Period size: 273 Copynumber: 1.9 Consensus size: 272
19390833 GTAGTTTCTG
* * * * * * **
19390843 AAAAATTAATTTTGAGAAGATACTTCTGAAAAGATAATGTCAAACACGCTTCAAGCAGGATGTAC
1 AAAAAATAATTTAGAGAAGACACTTCTGAAAAAATAATGTCAAAAACGCTTCAAACAGGATACAC
* * * * * *
19390908 TGTCAGCAAAAGTACTAAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAATAGTTCTTGAAAA
66 TGTCAACAAAAGTACTAAAAAAAGCTCACACATGGACGCTATTTTTCTACAATAGATCCTGAAAA
* * *
19390973 AATAATTTTGAGAAGACAGTTTTGAAAAAATAGTGTCAAAAACGCTTCAATCAGGATGCACTGTC
131 AATAATTTAGAGAAGACAGTTATGAAAAAATAGTGTCAAAAACGCTTCAAACAGGATGCACTGTC
* * *
19391038 AGCAAAATTACTGAAAAAAGCTTCCACGTGGACGCTCTTTTTCTACAGTAGTTCCTGAAAAAATA
196 AGCAAAATTACTAAAAAAAGCTTCCACGTGGACGCACTTTTTCTAAAGTAGTTCCTGAAAAAATA
19391103 ATTTTGAGAAGA
261 ATTTTGAGAAGA
** *
19391115 AAAAAATAATTTAGAGAAGACGGTTCTGAAAAAAATAGTGTCAAAAACGCTTCAAACAGGATACA
1 AAAAAATAATTTAGAGAAGACACTTCTG-AAAAAATAATGTCAAAAACGCTTCAAACAGGATACA
* * * *
19391180 CTGTCAACAAAATTACTGAAAAAAGCCTCATACAT-GACGCTATTTTTCTACAGTAGATCCTGAA
65 CTGTCAACAAAAGTACTAAAAAAAG-CTCACACATGGACGCTATTTTTCTACAATAGATCCTGAA
** * * *
19391244 AAAATAATTTAGAGAAGATGGTTATGAAGAAATAGTGTTAAAAACGCTTCAAAGAGGATGCACTG
129 AAAATAATTTAGAGAAGACAGTTATGAAAAAATAGTGTCAAAAACGCTTCAAACAGGATGCACTG
* *
19391309 TTAGCAAAATTACTAAAAAAAGCTTCCAGGTGGACGCACTTTTTCTAAAGTAGTTCCTG
194 TCAGCAAAATTACTAAAAAAAGCTTCCACGTGGACGCACTTTTTCTAAAGTAGTTCCTG
19391368 CTTGGCCTTA
Statistics
Matches: 217, Mismatches: 34, Indels: 3
0.85 0.13 0.01
Matches are distributed among these distances:
272 23 0.11
273 188 0.87
274 6 0.03
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Consensus pattern (272 bp):
AAAAAATAATTTAGAGAAGACACTTCTGAAAAAATAATGTCAAAAACGCTTCAAACAGGATACAC
TGTCAACAAAAGTACTAAAAAAAGCTCACACATGGACGCTATTTTTCTACAATAGATCCTGAAAA
AATAATTTAGAGAAGACAGTTATGAAAAAATAGTGTCAAAAACGCTTCAAACAGGATGCACTGTC
AGCAAAATTACTAAAAAAAGCTTCCACGTGGACGCACTTTTTCTAAAGTAGTTCCTGAAAAAATA
ATTTTGAGAAGA
Found at i:19393357 original size:42 final size:42
Alignment explanation
Indices: 19393289--19393409 Score: 170
Period size: 42 Copynumber: 2.9 Consensus size: 42
19393279 TTAACTCATA
* * *
19393289 TGAGTTTCTATTTAACCCTAATGGGTTTCCGTTTAGCTCTTT
1 TGAGCTTCAATTTAACCCTTATGGGTTTCCGTTTAGCTCTTT
* *
19393331 TGAGCTTCAATTTAACCCTTATGGGTTTCCATTCAGCTCTTT
1 TGAGCTTCAATTTAACCCTTATGGGTTTCCGTTTAGCTCTTT
* * *
19393373 TGAGCTTCCATTCAACCCTTATGGGTTTCTGTTTAGC
1 TGAGCTTCAATTTAACCCTTATGGGTTTCCGTTTAGC
19393410 ACTTATGTGC
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.44
Consensus pattern (42 bp):
TGAGCTTCAATTTAACCCTTATGGGTTTCCGTTTAGCTCTTT
Found at i:19393383 original size:21 final size:21
Alignment explanation
Indices: 19393323--19393386 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
19393313 GTTTCCGTTT
* *
19393323 AGCTCTTTTGAGCTTCAATTT
1 AGCTCTTTTGAGCTTCCATTC
* * * * *
19393344 AACCCTTATGGGTTTCCATTC
1 AGCTCTTTTGAGCTTCCATTC
19393365 AGCTCTTTTGAGCTTCCATTC
1 AGCTCTTTTGAGCTTCCATTC
19393386 A
1 A
19393387 ACCCTTATGG
Statistics
Matches: 31, Mismatches: 12, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.19, C:0.25, G:0.14, T:0.42
Consensus pattern (21 bp):
AGCTCTTTTGAGCTTCCATTC
Found at i:19396646 original size:40 final size:40
Alignment explanation
Indices: 19396591--19396818 Score: 321
Period size: 40 Copynumber: 5.7 Consensus size: 40
19396581 GGTGCTCAGA
19396591 CGAGCCATACCTAGTGAATCTATTGAAACGTATGCGCTTT
1 CGAGCCATACCTAGTGAATCTATTGAAACGTATGCGCTTT
* ** *
19396631 CGAGCCATACCTAGTGAATCTATTTAAACAAATGTGCTTT
1 CGAGCCATACCTAGTGAATCTATTGAAACGTATGCGCTTT
* * *
19396671 CGAGCCATACCTAGTGAATCTACTAAAACGTATGCACTTT
1 CGAGCCATACCTAGTGAATCTATTGAAACGTATGCGCTTT
* *
19396711 CGAGCCATACCTAGTGAATCTATTGAAATGTATGTGCTTT
1 CGAGCCATACCTAGTGAATCTATTGAAACGTATGCGCTTT
* * *
19396751 CGAGCCATACCTAGTGAATATACTAAAACGTATGCGCTTT
1 CGAGCCATACCTAGTGAATCTATTGAAACGTATGCGCTTT
* * *
19396791 CAAGCTATACCTACTGAATCTATTGAAA
1 CGAGCCATACCTAGTGAATCTATTGAAA
19396819 GAATGCTCTA
Statistics
Matches: 162, Mismatches: 26, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 162 1.00
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (40 bp):
CGAGCCATACCTAGTGAATCTATTGAAACGTATGCGCTTT
Found at i:19396684 original size:80 final size:80
Alignment explanation
Indices: 19396591--19396818 Score: 357
Period size: 80 Copynumber: 2.9 Consensus size: 80
19396581 GGTGCTCAGA
* * *
19396591 CGAGCCATACCTAGTGAATCTATTGAAACGTATGCGCTTTCGAGCCATACCTAGTGAATCTATTT
1 CGAGCCATACCTAGTGAATCTACTAAAACGTATGCGCTTTCGAGCCATACCTAGTGAATCTATTG
19396656 AAACAAATGTGCTTT
66 AAACAAATGTGCTTT
*
19396671 CGAGCCATACCTAGTGAATCTACTAAAACGTATGCACTTTCGAGCCATACCTAGTGAATCTATTG
1 CGAGCCATACCTAGTGAATCTACTAAAACGTATGCGCTTTCGAGCCATACCTAGTGAATCTATTG
***
19396736 AAATGTATGTGCTTT
66 AAACAAATGTGCTTT
* * * *
19396751 CGAGCCATACCTAGTGAATATACTAAAACGTATGCGCTTTCAAGCTATACCTACTGAATCTATTG
1 CGAGCCATACCTAGTGAATCTACTAAAACGTATGCGCTTTCGAGCCATACCTAGTGAATCTATTG
19396816 AAA
66 AAA
19396819 GAATGCTCTA
Statistics
Matches: 136, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
80 136 1.00
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (80 bp):
CGAGCCATACCTAGTGAATCTACTAAAACGTATGCGCTTTCGAGCCATACCTAGTGAATCTATTG
AAACAAATGTGCTTT
Found at i:19397274 original size:20 final size:20
Alignment explanation
Indices: 19397229--19397274 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
19397219 TGTTTATTTC
19397229 TCTTTTTAGTTGTTTTGTTT
1 TCTTTTTAGTTGTTTTGTTT
*
19397249 TATTTTTA-TT-TTCTTGTATT
1 TCTTTTTAGTTGTT-TTGT-TT
19397269 TCTTTT
1 TCTTTT
19397275 AATTATTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 2 0.09
19 6 0.27
20 14 0.64
ACGTcount: A:0.09, C:0.07, G:0.09, T:0.76
Consensus pattern (20 bp):
TCTTTTTAGTTGTTTTGTTT
Found at i:19400841 original size:34 final size:33
Alignment explanation
Indices: 19400798--19400891 Score: 116
Period size: 34 Copynumber: 2.7 Consensus size: 33
19400788 GAATTTTTTT
19400798 TAAATTTAATTAAATTAAGTTTTAGGGGTTTTAAG
1 TAAA-TTAATTAAATTAAG-TTTAGGGGTTTTAAG
* *
19400833 TAAATTAATTAAAATAAAGTTTAGGGTTTTTAAG
1 TAAATTAATT-AAATTAAGTTTAGGGGTTTTAAG
* *
19400867 AAAATTAATTAAATTAGGGTTTAGG
1 TAAATTAATTAAATTA-AGTTTAGG
19400892 TTTTAAAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
33 5 0.10
34 36 0.69
35 11 0.21
ACGTcount: A:0.41, C:0.00, G:0.17, T:0.41
Consensus pattern (33 bp):
TAAATTAATTAAATTAAGTTTAGGGGTTTTAAG
Found at i:19401362 original size:126 final size:126
Alignment explanation
Indices: 19401118--19401527 Score: 572
Period size: 126 Copynumber: 3.3 Consensus size: 126
19401108 CGTGGACGCT
* * * * *
19401118 ACGTGGACGC-CTTTTTCTACAATAGTTCTTGAAAAAATAATTTTGAGAAGACAGTTTTGAAAAA
1 ACGTGGACGCTCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTAGAGAAGACGGTTATGAAAAA
*
19401182 ATAGTGTCAAAAACGCTTCAAGCAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTTCC
66 ATAGTGTCAAAAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTTCC
* *
19401243 ACGTGGATGCTCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTAGAGAAGACGGTTCTGAAAAA
1 ACGTGGACGCTCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTAGAGAAGACGGTTATG-AAAA
* * * *
19401308 AATAGTGTCAAAAACGCTTCAAACAGGATACACTGTCAACAAAATTACTGAAAAAAGC-TCAT
65 AATAGTGTCAAAAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTTC-C
* * * * * *
19401370 ACATGAACGCTATTTTTCTACAGTAGATCCTGAAAAAATAATTTAGAGAAGATGGTTATGAAGAA
1 ACGTGGACGCTCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTAGAGAAGACGGTTATGAAAAA
* * *
19401435 ATAGTGTTAAAAACGCTTCAAGCAGGATGCACTGTTAGCAAAATTACTAAAAAAAGCTTCC
66 ATAGTGTCAAAAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTTCC
* * *
19401496 AGGTGGACGCACTTTTTCTAAAGTAGTTCCTG
1 ACGTGGACGCTCTTTTTCTACAGTAGTTCCTG
19401528 CTTGGCCTTA
Statistics
Matches: 248, Mismatches: 33, Indels: 7
0.86 0.11 0.02
Matches are distributed among these distances:
125 9 0.04
126 126 0.51
127 113 0.46
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (126 bp):
ACGTGGACGCTCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTAGAGAAGACGGTTATGAAAAA
ATAGTGTCAAAAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTTCC
Found at i:19401449 original size:253 final size:257
Alignment explanation
Indices: 19400991--19401527 Score: 672
Period size: 253 Copynumber: 2.1 Consensus size: 257
19400981 GATTTTGTTT
* * * * *
19400991 TCTTTTTCTACAGTAGTTTCTGAAAAATTAATTTTGAGAAGATACTTCTGAAAAGATAATGTCAA
1 TCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTAGAGAAGACACTTCTGAAAAAATAATGTCAA
* * ** *
19401056 ACACGCTTCAAGCAGGATGTACTGTCAGCAAAAGTACTAAAAAAAGCTCCCACGTGGACGCTACG
66 AAACGCTTCAAACAGGATACACTGTCAACAAAAGTACTAAAAAAAGCT-CCAC-T-GAC-CTAC-
* * * * * *
19401121 TGGACGCCTTTTTCTACAATAGTTCTTGAAAAAATAATTTTGAGAAGACAGTTTTGAAAAAATAG
126 TGAACGCATTTTTCTACAATAGATCCTGAAAAAATAATTTAGAGAAGACAGTTATGAAAAAATAG
* *
19401186 TGTCAAAAACGCTTCAAGCAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTTCCACGTGGAT
191 TGTCAAAAACGCTTCAAGCAGGATGCACTATCAGCAAAATTACTAAAAAAAGCTTCCACGTGGAC
19401251 GC
256 GC
** *
19401253 TCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTAGAGAAGACGGTTCTGAAAAAAATAGTGTCA
1 TCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTAGAGAAGACACTTCTG-AAAAAATAATGTCA
* *
19401318 AAAACGCTTCAAACAGGATACACTGTCAACAAAATTACTGAAAAAAGCT-CA-T-A-C-A-TGAA
65 AAAACGCTTCAAACAGGATACACTGTCAACAAAAGTACTAAAAAAAGCTCCACTGACCTACTGAA
* ** *
19401377 CGCTATTTTTCTACAGTAGATCCTGAAAAAATAATTTAGAGAAGATGGTTATGAAGAAATAGTGT
130 CGC-ATTTTTCTACAATAGATCCTGAAAAAATAATTTAGAGAAGACAGTTATGAAAAAATAGTGT
* * * *
19401442 TAAAAACGCTTCAAGCAGGATGCACTGTTAGCAAAATTACTAAAAAAAGCTTCCAGGTGGACGC
194 CAAAAACGCTTCAAGCAGGATGCACTATCAGCAAAATTACTAAAAAAAGCTTCCACGTGGACGC
* *
19401506 ACTTTTTCTAAAGTAGTTCCTG
1 TCTTTTTCTACAGTAGTTCCTG
19401528 CTTGGCCTTA
Statistics
Matches: 240, Mismatches: 33, Indels: 13
0.84 0.12 0.05
Matches are distributed among these distances:
252 6 0.03
253 130 0.54
254 1 0.00
255 1 0.00
257 1 0.00
259 1 0.00
261 2 0.01
262 44 0.18
263 54 0.22
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.28
Consensus pattern (257 bp):
TCTTTTTCTACAGTAGTTCCTGAAAAAATAATTTAGAGAAGACACTTCTGAAAAAATAATGTCAA
AAACGCTTCAAACAGGATACACTGTCAACAAAAGTACTAAAAAAAGCTCCACTGACCTACTGAAC
GCATTTTTCTACAATAGATCCTGAAAAAATAATTTAGAGAAGACAGTTATGAAAAAATAGTGTCA
AAAACGCTTCAAGCAGGATGCACTATCAGCAAAATTACTAAAAAAAGCTTCCACGTGGACGC
Found at i:19403479 original size:42 final size:42
Alignment explanation
Indices: 19403422--19403555 Score: 144
Period size: 42 Copynumber: 3.2 Consensus size: 42
19403412 TTCCATTTAG
* * *
19403422 CTCTCATGAGCTTCAGTTTAACCC-TATTGGGTTTTTGTTCAG
1 CTCTTATGAGCTTCAGTTTAACCCTTA-TGGGTTTCTGTTCAA
* *
19403464 CTCTTTTGAGCTTCAGTTTCACCCTTATGGGTTTCTGTTCAA
1 CTCTTATGAGCTTCAGTTTAACCCTTATGGGTTTCTGTTCAA
* * * * * *
19403506 CTCTTATGAGCTTCCGTTCAACTCTTATGAGCTTCCGTTCAA
1 CTCTTATGAGCTTCAGTTTAACCCTTATGGGTTTCTGTTCAA
*
19403548 CCCTTATG
1 CTCTTATG
19403556 GGTTTCTGTT
Statistics
Matches: 77, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
42 75 0.97
43 2 0.03
ACGTcount: A:0.16, C:0.25, G:0.16, T:0.42
Consensus pattern (42 bp):
CTCTTATGAGCTTCAGTTTAACCCTTATGGGTTTCTGTTCAA
Found at i:19403511 original size:21 final size:21
Alignment explanation
Indices: 19403458--19403555 Score: 108
Period size: 21 Copynumber: 4.7 Consensus size: 21
19403448 TTGGGTTTTT
* * *
19403458 GTTCAGCTCTTTTGAGCTTCA
1 GTTCAACTCTTATGAGCTTCC
* * * *
19403479 GTTTC-ACCCTTATGGGTTTCT
1 G-TTCAACTCTTATGAGCTTCC
19403500 GTTCAACTCTTATGAGCTTCC
1 GTTCAACTCTTATGAGCTTCC
19403521 GTTCAACTCTTATGAGCTTCC
1 GTTCAACTCTTATGAGCTTCC
*
19403542 GTTCAACCCTTATG
1 GTTCAACTCTTATG
19403556 GGTTTCTGTT
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
20 3 0.05
21 58 0.91
22 3 0.05
ACGTcount: A:0.16, C:0.27, G:0.16, T:0.41
Consensus pattern (21 bp):
GTTCAACTCTTATGAGCTTCC
Found at i:19403575 original size:63 final size:63
Alignment explanation
Indices: 19403458--19403576 Score: 168
Period size: 63 Copynumber: 1.9 Consensus size: 63
19403448 TTGGGTTTTT
* * *
19403458 GTTCAGCTCTTTTGAGCTTCAGTTTCACCCTTATGGGTTTCTGTTCAACTCTTATGAGCTTCC
1 GTTCAACTCTTATGAGCTTCAGTTTCACCCTTATGGGTTTCTGTTCAACACTTATGAGCTTCC
* * *
19403521 GTTCAACTCTTATGAGCTTCCG-TTCAACCCTTATGGGTTTCTGTTTAGCACTTATG
1 GTTCAACTCTTATGAGCTTCAGTTTC-ACCCTTATGGGTTTCTGTTCAACACTTATG
19403577 TTCTTCTGTG
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
62 3 0.06
63 46 0.94
ACGTcount: A:0.16, C:0.24, G:0.18, T:0.42
Consensus pattern (63 bp):
GTTCAACTCTTATGAGCTTCAGTTTCACCCTTATGGGTTTCTGTTCAACACTTATGAGCTTCC
Found at i:19407933 original size:18 final size:18
Alignment explanation
Indices: 19407912--19407946 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19407902 AAGGAAACAC
*
19407912 ATAAATGTTAGGATACAT
1 ATAAAGGTTAGGATACAT
*
19407930 ATAAGGGTTAGGATACA
1 ATAAAGGTTAGGATACA
19407947 CACTGGTATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.06, G:0.23, T:0.29
Consensus pattern (18 bp):
ATAAAGGTTAGGATACAT
Found at i:19408625 original size:5 final size:5
Alignment explanation
Indices: 19408617--19408642 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
19408607 GAGATGGAAT
19408617 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
19408643 ATATTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:19408642 original size:26 final size:26
Alignment explanation
Indices: 19408591--19408642 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
19408581 TGAAGTTTTC
* * *
19408591 TCGAATCGAGTCGAGTGAGATGGAAT
1 TCGAATCGAATCGAATGAGATCGAAT
19408617 TCGAATCGAATCGAATCGA-ATCGAAT
1 TCGAATCGAATCGAAT-GAGATCGAAT
19408643 ATATTTGTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (26 bp):
TCGAATCGAATCGAATGAGATCGAAT
Found at i:19409293 original size:21 final size:21
Alignment explanation
Indices: 19409259--19409299 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
19409249 GGGGGAAAGT
*
19409259 GGGAAGAAGTAAAAGTTTTGA
1 GGGAAGAAGTAAAAGGTTTGA
19409280 GGGAA-AAGTAAAAAGGTTTG
1 GGGAAGAAGT-AAAAGGTTTG
19409300 GGAGTTTGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.44, C:0.00, G:0.34, T:0.22
Consensus pattern (21 bp):
GGGAAGAAGTAAAAGGTTTGA
Found at i:19409354 original size:9 final size:9
Alignment explanation
Indices: 19409337--19409373 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
19409327 TATAGTTTGA
19409337 TATTCGAAT
1 TATTCGAAT
*
19409346 TATTTGAAT
1 TATTCGAAT
*
19409355 TATTCGAGT
1 TATTCGAAT
19409364 TATTCGAAT
1 TATTCGAAT
19409373 T
1 T
19409374 TGAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:19417384 original size:1 final size:1
Alignment explanation
Indices: 19417378--19417407 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
19417368 CATGCACGTC
19417378 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
19417408 ACAATAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:19428898 original size:6 final size:6
Alignment explanation
Indices: 19428887--19428911 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
19428877 TGTGGGTGAT
19428887 TGATGG TGATGG TGATGG TGATGG T
1 TGATGG TGATGG TGATGG TGATGG T
19428912 CTTCTTGCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.48, T:0.36
Consensus pattern (6 bp):
TGATGG
Found at i:19434245 original size:12 final size:12
Alignment explanation
Indices: 19434228--19434252 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19434218 AACTCTGTAG
19434228 CTAGTTTAAATT
1 CTAGTTTAAATT
19434240 CTAGTTTAAATT
1 CTAGTTTAAATT
19434252 C
1 C
19434253 GATTTTAAAA
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:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (12 bp):
CTAGTTTAAATT
Found at i:19442654 original size:13 final size:13
Alignment explanation
Indices: 19442636--19442660 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19442626 TTTCTCTCTT
19442636 AAGCTGGATGTTC
1 AAGCTGGATGTTC
19442649 AAGCTGGATGTT
1 AAGCTGGATGTT
19442661 AATTTGCCTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.12, G:0.32, T:0.32
Consensus pattern (13 bp):
AAGCTGGATGTTC
Found at i:19455586 original size:25 final size:25
Alignment explanation
Indices: 19455527--19455587 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
19455517 AGCTCATATA
* *
19455527 AGCTTACCGATACTCAGCTCGCATG
1 AGCTTACCGTTACTCAGCTCGCAGG
* * *
19455552 AGCTTGCCGTTATTCAGCTCGGAGG
1 AGCTTACCGTTACTCAGCTCGCAGG
19455577 AGCTTACCGTT
1 AGCTTACCGTT
19455588 TATAGCTCGA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.20, C:0.28, G:0.25, T:0.28
Consensus pattern (25 bp):
AGCTTACCGTTACTCAGCTCGCAGG
Found at i:19470363 original size:855 final size:855
Alignment explanation
Indices: 19468713--19470423 Score: 3422
Period size: 855 Copynumber: 2.0 Consensus size: 855
19468703 ACATTTTGCA
19468713 CATTACTGCTTTAATTTACCGCTGCATACTTAAGTTGGTGTCATAACATTAATTATAATTTGTTA
1 CATTACTGCTTTAATTTACCGCTGCATACTTAAGTTGGTGTCATAACATTAATTATAATTTGTTA
19468778 TAATAACTTGACCACTTTTGTAATGACCATATCGAGTACGAAATGCAGTTTTTGGAACATCACTT
66 TAATAACTTGACCACTTTTGTAATGACCATATCGAGTACGAAATGCAGTTTTTGGAACATCACTT
19468843 TCTTTTACTTTCAGCTGATAATACCCAGATCTCAAGTCAATCTTCAAAAATACCGAAGCACCTTT
131 TCTTTTACTTTCAGCTGATAATACCCAGATCTCAAGTCAATCTTCAAAAATACCGAAGCACCTTT
19468908 TAGCTGATCAAATAAATCATCTATACGGGGTAATGGATACCGGTTCTTGATCGTCACTTTATTTA
196 TAGCTGATCAAATAAATCATCTATACGGGGTAATGGATACCGGTTCTTGATCGTCACTTTATTTA
19468973 ACTGCCGATAATCAATACAAAGCCGCATTGATCCATCTTTCTTCTTAACAAATAACATTGGAGCT
261 ACTGCCGATAATCAATACAAAGCCGCATTGATCCATCTTTCTTCTTAACAAATAACATTGGAGCT
19469038 CCCCAAGGTGAAATACTCGGTCTAATGAATCCACGATCTAGTAAGTCCTGTAACTGCACCTTCAA
326 CCCCAAGGTGAAATACTCGGTCTAATGAATCCACGATCTAGTAAGTCCTGTAACTGCACCTTCAA
19469103 CTCTTTTAATTGTAGGGGGTTTTATGTAAAAATAAGCAGAAATGCTGTCGAAATTTTTTTTAAAA
391 CTCTTTTAATTGTAGGGGGTTTTATGTAAAAATAAGCAGAAATGCTGTCGAAATTTTTTTTAAAA
19469168 AAAATGAAACCAATTAGCATAAATTTATATGAATTTATAATTCTTTTATATATGTTCGTTATTTA
456 AAAATGAAACCAATTAGCATAAATTTATATGAATTTATAATTCTTTTATATATGTTCGTTATTTA
19469233 ATTAAGAATTATTTGTAAATTGTTTGATATGTCCGGTAATACCTTGTAACCCTATTCTAGCGACG
521 ATTAAGAATTATTTGTAAATTGTTTGATATGTCCGGTAATACCTTGTAACCCTATTCTAGCGACG
19469298 GTTTGGGGTTAGGGGGTGTTACAATTGTTAGTATTAGAGCTTTACAGGTTTAGCCAATTCTCGGA
586 GTTTGGGGTTAGGGGGTGTTACAATTGTTAGTATTAGAGCTTTACAGGTTTAGCCAATTCTCGGA
19469363 CTAAATCGAGCTCGGAATTGAGTCTAGAGGTACATGCCTTAATTGAGTCGAGTTGAGTCGGGATT
651 CTAAATCGAGCTCGGAATTGAGTCTAGAGGTACATGCCTTAATTGAGTCGAGTTGAGTCGGGATT
19469428 TGGATGCTGATATATTTGTTTTTGTTTTATAGTTGAAAATGTCGAATGATTATAATGATTATGAT
716 TGGATGCTGATATATTTGTTTTTGTTTTATAGTTGAAAATGTCGAATGATTATAATGATTATGAT
19469493 AATGATAAATGTTATGTTATACTTGTGTATATATGAGAGTTAAATTTTGAGGCTTTACGACCTTC
781 AATGATAAATGTTATGTTATACTTGTGTATATATGAGAGTTAAATTTTGAGGCTTTACGACCTTC
19469558 ACCCATTCGC
846 ACCCATTCGC
19469568 CATTACTGCTTTAATTTACCGCTGCATACTTAAGTTGGTGTCATAACATTAATTATAATTTGTTA
1 CATTACTGCTTTAATTTACCGCTGCATACTTAAGTTGGTGTCATAACATTAATTATAATTTGTTA
19469633 TAATAACTTGACCACTTTTGTAATGACCATATCGAGTACGAAATGCAGTTTTTGGAACATCACTT
66 TAATAACTTGACCACTTTTGTAATGACCATATCGAGTACGAAATGCAGTTTTTGGAACATCACTT
19469698 TCTTTTACTTTCAGCTGATAATACCCAGATCTCAAGTCAATCTTCAAAAATACCGAAGCACCTTT
131 TCTTTTACTTTCAGCTGATAATACCCAGATCTCAAGTCAATCTTCAAAAATACCGAAGCACCTTT
19469763 TAGCTGATCAAATAAATCATCTATACGGGGTAATGGATACCGGTTCTTGATCGTCACTTTATTTA
196 TAGCTGATCAAATAAATCATCTATACGGGGTAATGGATACCGGTTCTTGATCGTCACTTTATTTA
19469828 ACTGCCGATAATCAATACAAAGCCGCATTGATCCATCTTTCTTCTTAACAAATAACATTGGAGCT
261 ACTGCCGATAATCAATACAAAGCCGCATTGATCCATCTTTCTTCTTAACAAATAACATTGGAGCT
19469893 CCCCAAGGTGAAATACTCGGTCTAATGAATCCACGATCTAGTAAGTCCTGTAACTGCACCTTCAA
326 CCCCAAGGTGAAATACTCGGTCTAATGAATCCACGATCTAGTAAGTCCTGTAACTGCACCTTCAA
19469958 CTCTTTTAATTGTAGGGGGTTTTATGTAAAAATAAGCAGAAATGCTGTCGAAATTTTTTTTAAAA
391 CTCTTTTAATTGTAGGGGGTTTTATGTAAAAATAAGCAGAAATGCTGTCGAAATTTTTTTTAAAA
19470023 AAAATGAAACCAATTAGCATAAATTTATATGAATTTATAATTCTTTTATATATGTTCGTTATTTA
456 AAAATGAAACCAATTAGCATAAATTTATATGAATTTATAATTCTTTTATATATGTTCGTTATTTA
19470088 ATTAAGAATTATTTGTAAATTGTTTGATATGTCCGGTAATACCTTGTAACCCTATTCTAGCGACG
521 ATTAAGAATTATTTGTAAATTGTTTGATATGTCCGGTAATACCTTGTAACCCTATTCTAGCGACG
19470153 GTTTGGGGTTAGGGGGTGTTACAATTGTTAGTATTAGAGCTTTACAGGTTTAGCCAATTCTCGGA
586 GTTTGGGGTTAGGGGGTGTTACAATTGTTAGTATTAGAGCTTTACAGGTTTAGCCAATTCTCGGA
19470218 CTAAATCGAGCTCGGAATTGAGTCTAGAGGTACATGCCTTAATTGAGTCGAGTTGAGTCGGGATT
651 CTAAATCGAGCTCGGAATTGAGTCTAGAGGTACATGCCTTAATTGAGTCGAGTTGAGTCGGGATT
19470283 TGGATGCTGATATATTTGTTTTTGTTTTATAGTTGAAAATGTCGAATGATTATAATGATTATGAT
716 TGGATGCTGATATATTTGTTTTTGTTTTATAGTTGAAAATGTCGAATGATTATAATGATTATGAT
19470348 AATGATAAATGTTATGTTATACTTGTGTATATATGAGAGTTAAATTTTGAGGCTTTACGACCTTC
781 AATGATAAATGTTATGTTATACTTGTGTATATATGAGAGTTAAATTTTGAGGCTTTACGACCTTC
19470413 ACCCATTCGC
846 ACCCATTCGC
19470423 C
1 C
19470424 TGTACAATGG
Statistics
Matches: 856, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
855 856 1.00
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (855 bp):
CATTACTGCTTTAATTTACCGCTGCATACTTAAGTTGGTGTCATAACATTAATTATAATTTGTTA
TAATAACTTGACCACTTTTGTAATGACCATATCGAGTACGAAATGCAGTTTTTGGAACATCACTT
TCTTTTACTTTCAGCTGATAATACCCAGATCTCAAGTCAATCTTCAAAAATACCGAAGCACCTTT
TAGCTGATCAAATAAATCATCTATACGGGGTAATGGATACCGGTTCTTGATCGTCACTTTATTTA
ACTGCCGATAATCAATACAAAGCCGCATTGATCCATCTTTCTTCTTAACAAATAACATTGGAGCT
CCCCAAGGTGAAATACTCGGTCTAATGAATCCACGATCTAGTAAGTCCTGTAACTGCACCTTCAA
CTCTTTTAATTGTAGGGGGTTTTATGTAAAAATAAGCAGAAATGCTGTCGAAATTTTTTTTAAAA
AAAATGAAACCAATTAGCATAAATTTATATGAATTTATAATTCTTTTATATATGTTCGTTATTTA
ATTAAGAATTATTTGTAAATTGTTTGATATGTCCGGTAATACCTTGTAACCCTATTCTAGCGACG
GTTTGGGGTTAGGGGGTGTTACAATTGTTAGTATTAGAGCTTTACAGGTTTAGCCAATTCTCGGA
CTAAATCGAGCTCGGAATTGAGTCTAGAGGTACATGCCTTAATTGAGTCGAGTTGAGTCGGGATT
TGGATGCTGATATATTTGTTTTTGTTTTATAGTTGAAAATGTCGAATGATTATAATGATTATGAT
AATGATAAATGTTATGTTATACTTGTGTATATATGAGAGTTAAATTTTGAGGCTTTACGACCTTC
ACCCATTCGC
Found at i:19488310 original size:31 final size:31
Alignment explanation
Indices: 19488274--19488332 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
19488264 AACTTTAATT
* *
19488274 CTTATACTTTTCGAATTGGTCAATTTTAGGC
1 CTTATACTTTTCAAATTGGTAAATTTTAGGC
*
19488305 CTTATACTTTTCAAATTTGTAAATTTTA
1 CTTATACTTTTCAAATTGGTAAATTTTA
19488333 ATGCTGACCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.27, C:0.14, G:0.10, T:0.49
Consensus pattern (31 bp):
CTTATACTTTTCAAATTGGTAAATTTTAGGC
Found at i:19496984 original size:3 final size:3
Alignment explanation
Indices: 19496881--19496965 Score: 68
Period size: 3 Copynumber: 27.7 Consensus size: 3
19496871 ATATTATCAC
* * *
19496881 AAT AAT AAT GAAT AAAT AA- AAG AAA AAT AA- AACT AAT AAT GAT CAAT
1 AAT AAT AAT -AAT -AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT -AAT
*
19496928 AAT AAT AGT AAT AAT AAT AAT AAT GAA- AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AA
19496966 AGTAATTAAC
Statistics
Matches: 68, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
2 6 0.09
3 50 0.74
4 12 0.18
ACGTcount: A:0.66, C:0.02, G:0.06, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:19499253 original size:58 final size:58
Alignment explanation
Indices: 19499163--19499279 Score: 216
Period size: 58 Copynumber: 2.0 Consensus size: 58
19499153 AATCAATGAA
* *
19499163 CACCTCTAGTTAGAAGGCTATGGGCTTGATTTGTCGGGTTTTAATATAGAGGATTAGT
1 CACCTCTAGGTAGAAGGCTATGGGCTTGATTTGTCAGGTTTTAATATAGAGGATTAGT
19499221 CACCTCTAGGTAGAAGGCTATGGGCTTGATTTGTCAGGTTTTAATATAGAGGATTAGT
1 CACCTCTAGGTAGAAGGCTATGGGCTTGATTTGTCAGGTTTTAATATAGAGGATTAGT
19499279 C
1 C
19499280 TTGATTGGGT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.25, C:0.13, G:0.27, T:0.35
Consensus pattern (58 bp):
CACCTCTAGGTAGAAGGCTATGGGCTTGATTTGTCAGGTTTTAATATAGAGGATTAGT
Found at i:19500871 original size:6 final size:6
Alignment explanation
Indices: 19500860--19500887 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
19500850 AACTCTAATT
19500860 TCCCAA TCCCAA TCCCAA TCCCAA TCCC
1 TCCCAA TCCCAA TCCCAA TCCCAA TCCC
19500888 GATTCATTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.29, C:0.54, G:0.00, T:0.18
Consensus pattern (6 bp):
TCCCAA
Found at i:19506698 original size:61 final size:61
Alignment explanation
Indices: 19506603--19506724 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
19506593 GAGAGCCTTC
19506603 ATTTCTTCCATCACGGCTTGTCTCCACTCAGCTGATTCAAGAGCCTCTTCTATATTTTTTG
1 ATTTCTTCCATCACGGCTTGTCTCCACTCAGCTGATTCAAGAGCCTCTTCTATATTTTTTG
19506664 ATTTCTTCCATCACGGCTTGTCTCCACTCAGCTGATTCAAGAGCCTCTTCTATATTTTTTG
1 ATTTCTTCCATCACGGCTTGTCTCCACTCAGCTGATTCAAGAGCCTCTTCTATATTTTTTG
19506725 GAGTTTTTAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.18, C:0.28, G:0.13, T:0.41
Consensus pattern (61 bp):
ATTTCTTCCATCACGGCTTGTCTCCACTCAGCTGATTCAAGAGCCTCTTCTATATTTTTTG
Found at i:19514114 original size:2 final size:2
Alignment explanation
Indices: 19514107--19514135 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
19514097 AATAGAGAAC
19514107 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19514136 GCTGGAATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19515319 original size:2 final size:2
Alignment explanation
Indices: 19515312--19515346 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
19515302 TCCATGGTGA
19515312 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19515347 NNNNNNNNNN
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19517190 original size:71 final size:72
Alignment explanation
Indices: 19517099--19517241 Score: 279
Period size: 71 Copynumber: 2.0 Consensus size: 72
19517089 ATGATAAAAA
19517099 AATCAAAATTATTTAAAAATAAAAAATACTATATAAAAATTCTAGAAAAATAAAATCTAAAATAT
1 AATCAAAATTATTTAAAAATAAAAAATACTATATAAAAATTCTAGAAAAATAAAATCTAAAATAT
19517164 TTTTGGT
66 TTTTGGT
19517171 AATCAAAATT-TTTAAAAATAAAAAATACTATATAAAAATTCTAGAAAAATAAAATCTAAAATAT
1 AATCAAAATTATTTAAAAATAAAAAATACTATATAAAAATTCTAGAAAAATAAAATCTAAAATAT
19517235 TTTTGGT
66 TTTTGGT
19517242 TGAAGAACTA
Statistics
Matches: 71, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
71 61 0.86
72 10 0.14
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.34
Consensus pattern (72 bp):
AATCAAAATTATTTAAAAATAAAAAATACTATATAAAAATTCTAGAAAAATAAAATCTAAAATAT
TTTTGGT
Found at i:19517222 original size:31 final size:31
Alignment explanation
Indices: 19517113--19517224 Score: 82
Period size: 31 Copynumber: 3.3 Consensus size: 31
19517103 AAAATTATTT
19517113 AAAAATAAAAAATACTATATAAAAATTCTAG
1 AAAAATAAAAAATACTATATAAAAATTCTAG
* * * **
19517144 AAAAATAAAATCTAAAATATTTTTGGTAATCAAAATT-TTT
1 AAAAAT--AA---AAAATA---CT-AT-ATAAAAATTCTAG
19517184 AAAAATAAAAAATACTATATAAAAATTCTAG
1 AAAAATAAAAAATACTATATAAAAATTCTAG
19517215 AAAAATAAAA
1 AAAAATAAAA
19517225 TCTAAAATAT
Statistics
Matches: 60, Mismatches: 10, Indels: 22
0.65 0.11 0.24
Matches are distributed among these distances:
30 8 0.13
31 18 0.30
32 1 0.02
33 2 0.03
35 6 0.10
36 6 0.10
38 2 0.03
39 1 0.02
40 8 0.13
41 8 0.13
ACGTcount: A:0.62, C:0.05, G:0.04, T:0.29
Consensus pattern (31 bp):
AAAAATAAAAAATACTATATAAAAATTCTAG
Found at i:19526365 original size:21 final size:21
Alignment explanation
Indices: 19526309--19526390 Score: 85
Period size: 21 Copynumber: 3.9 Consensus size: 21
19526299 TGATCAGTAA
*
19526309 ACGACACAT-AAGTGCCTGAA
1 ACGACACATAAAGTGCCTGAT
** *
19526329 ACGACACACGAGGTGCCTGAT
1 ACGACACATAAAGTGCCTGAT
*
19526350 ACGACACATAAAGTGCTTGATGT
1 ACGACACATAAAGTGCCTGA--T
*
19526373 ATGACACATAAAGTGCCT
1 ACGACACATAAAGTGCCT
19526391 AATCGGTAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
20 8 0.16
21 25 0.50
23 17 0.34
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (21 bp):
ACGACACATAAAGTGCCTGAT
Found at i:19526756 original size:16 final size:16
Alignment explanation
Indices: 19526730--19526769 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
19526720 TTAATAATAA
*
19526730 TACTTATCTTA-TATT
1 TACTTACCTTATTATT
19526745 TCACTTACCTTATTATT
1 T-ACTTACCTTATTATT
19526762 TACTTACC
1 TACTTACC
19526770 ATACACATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 16 0.73
17 5 0.23
ACGTcount: A:0.25, C:0.23, G:0.00, T:0.53
Consensus pattern (16 bp):
TACTTACCTTATTATT
Found at i:19531781 original size:18 final size:18
Alignment explanation
Indices: 19531720--19531790 Score: 63
Period size: 18 Copynumber: 3.7 Consensus size: 18
19531710 TTCATTTATC
*
19531720 TAATAATATAATATCAATT
1 TAATAATA-AATATCTATT
*
19531739 AAATAATAATATTTAT-TATT
1 TAATAATAA-A--TATCTATT
19531759 ATAATAATAAATATCTATT
1 -TAATAATAAATATCTATT
*
19531778 TAATAACAAATAT
1 TAATAATAAATAT
19531791 AAATATTACA
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
18 16 0.37
19 12 0.28
20 4 0.09
21 11 0.26
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
TAATAATAAATATCTATT
Found at i:19532070 original size:22 final size:22
Alignment explanation
Indices: 19532045--19532089 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
19532035 TTAAAAACCC
*
19532045 TATT-TCTCCTTTTTCTTTCTTT
1 TATTCTCTCC-TTGTCTTTCTTT
*
19532067 TATTCTTTCCTTGTCTTTCTTT
1 TATTCTCTCCTTGTCTTTCTTT
19532089 T
1 T
19532090 TCTCCGTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.04, C:0.22, G:0.02, T:0.71
Consensus pattern (22 bp):
TATTCTCTCCTTGTCTTTCTTT
Found at i:19532115 original size:16 final size:17
Alignment explanation
Indices: 19532096--19532138 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
19532086 TTTTTCTCCG
19532096 TGTTTCGTTTCTA-TTC
1 TGTTTCGTTTCTATTTC
19532112 TGTTTC-TTTCTATTTC
1 TGTTTCGTTTCTATTTC
*
19532128 T-TTTTGTTTCT
1 TGTTTCGTTTCT
19532139 TTTTGTTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 9 0.38
16 15 0.62
ACGTcount: A:0.05, C:0.16, G:0.09, T:0.70
Consensus pattern (17 bp):
TGTTTCGTTTCTATTTC
Found at i:19532147 original size:9 final size:10
Alignment explanation
Indices: 19532102--19532150 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
19532092 TCCGTGTTTC
*
19532102 GTTTCTATTCT
1 GTTTCT-TTTT
*
19532113 GTTTCTTTCT
1 GTTTCTTTTT
*
19532123 ATTTCTTTTT
1 GTTTCTTTTT
19532133 GTTTCTTTTT
1 GTTTCTTTTT
19532143 G-TTCTTTT
1 GTTTCTTTT
19532151 ATTTTACTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
9 7 0.20
10 22 0.63
11 6 0.17
ACGTcount: A:0.04, C:0.14, G:0.08, T:0.73
Consensus pattern (10 bp):
GTTTCTTTTT
Found at i:19532721 original size:133 final size:129
Alignment explanation
Indices: 19532519--19532759 Score: 410
Period size: 133 Copynumber: 1.8 Consensus size: 129
19532509 TTGTTTCTTC
* *
19532519 TTTTTTTACTAATTATTTATAAATAATACAAAAGTAATTAAATTAATACACTTGTATTTTATTTT
1 TTTTTTTACTAACTATATATAAATAATACAAAAGTAATTAAATTAATACACTTGTATTTTATTTT
*
19532584 TACCTTACACTTGTCTTTTCTTAATTTATTTCATAATATAATACTATAAATAAATAATAAAATA
66 TACCTTACACTTGTCATTTCTTAATTTATTTCATAATATAATACTATAAATAAATAATAAAATA
*
19532648 TTTTTTTACTAACTATATATAAATAATACAAATGTACTCATTTAAATTAATACACTTGTATTTTA
1 TTTTTTTACTAACTATATATAAATAATACAAAAGTA---A-TTAAATTAATACACTTGTATTTTA
19532713 TTTTTACCTTACACTTGTCATTTCTTAATTTATTTCATAATATAATA
62 TTTTTACCTTACACTTGTCATTTCTTAATTTATTTCATAATATAATA
19532760 TCAATTTAAT
Statistics
Matches: 104, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
129 33 0.32
132 1 0.01
133 70 0.67
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (129 bp):
TTTTTTTACTAACTATATATAAATAATACAAAAGTAATTAAATTAATACACTTGTATTTTATTTT
TACCTTACACTTGTCATTTCTTAATTTATTTCATAATATAATACTATAAATAAATAATAAAATA
Found at i:19532765 original size:23 final size:23
Alignment explanation
Indices: 19532739--19532787 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
19532729 GTCATTTCTT
*
19532739 AATTT-ATTTCATAATATAATATC
1 AATTTAATTT-ATAATATAATAGC
19532762 AATTTAATTTATAATATAATAGC
1 AATTTAATTTATAATATAATAGC
19532785 AAT
1 AAT
19532788 AATAACAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (23 bp):
AATTTAATTTATAATATAATAGC
Found at i:19539663 original size:98 final size:98
Alignment explanation
Indices: 19539494--19539688 Score: 363
Period size: 98 Copynumber: 2.0 Consensus size: 98
19539484 ATAATGAAAA
19539494 ACTTTAAAGGAACATCCACTTATCCAAGATTTAAGAAAACACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAGGAACATCCACTTATCCAAGATTTAAGAAAACACACCCAATACGTTAGGGCACGATT
*
19539559 CCTTTAGAATCCCAAACTCGGAATATTTCCTTC
66 CCTTTAGAATCCCAAACTCGGAAAATTTCCTTC
* *
19539592 ACTTTAAATGAACATCCGCTTATCCAAGATTTAAGAAAACACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAGGAACATCCACTTATCCAAGATTTAAGAAAACACACCCAATACGTTAGGGCACGATT
19539657 CCTTTAGAATCCCAAACTCGGAAAATTTCCTT
66 CCTTTAGAATCCCAAACTCGGAAAATTTCCTT
19539689 TATGATTCTT
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.36, C:0.25, G:0.12, T:0.27
Consensus pattern (98 bp):
ACTTTAAAGGAACATCCACTTATCCAAGATTTAAGAAAACACACCCAATACGTTAGGGCACGATT
CCTTTAGAATCCCAAACTCGGAAAATTTCCTTC
Done.