Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 51 of 106
Found at i:19247556 original size:2 final size:2
Alignment explanation
Indices: 19247549--19247578 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
19247539 AAAGATCTTA
19247549 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
19247579 CGTATNTAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:19248035 original size:511 final size:511
Alignment explanation
Indices: 19247074--19248095 Score: 2028
Period size: 511 Copynumber: 2.0 Consensus size: 511
19247064 TAGCTTTTGG
19247074 TAGTGTTTACTGCTTTGCTTTCATCTTTTACAATTTCTCATTAGACTAGTGGAATGTTTACATAC
1 TAGTGTTTACTGCTTTGCTTTCATCTTTTACAATTTCTCATTAGACTAGTGGAATGTTTACATAC
19247139 ATTTTTCATTAGACTAGTGTGCAATTTGTCTTGCATTTTGCACATTCCAGCCCAAACATGTGGGT
66 ATTTTTCATTAGACTAGTGTGCAATTTGTCTTGCATTTTGCACATTCCAGCCCAAACATGTGGGT
19247204 TGTCTTTGGTAGTCCTGCAAAGTAAATGTCTCCGTTACAGTATTTATAGCTTTTGAAGTAATCAA
131 TGTCTTTGGTAGTCCTGCAAAGTAAATGTCTCCGTTACAGTATTTATAGCTTTTGAAGTAATCAA
19247269 ATCATCACCTGGAGTTCAGGTGACAGATACAACTGGGTGTGCCACCACTCAAGAACCAATGATGG
196 ATCATCACCTGGAGTTCAGGTGACAGATACAACTGGGTGTGCCACCACTCAAGAACCAATGATGG
19247334 GAGTCAGGTTTATGTCACTTTTATATATATGATGAGAGATATATGTGTAGTTACCTGTAAAAATG
261 GAGTCAGGTTTATGTCACTTTTATATATATGATGAGAGATATATGTGTAGTTACCTGTAAAAATG
19247399 ATGTAAAAGGTTTGGTTATTGTGGATGTACACTCTCCCTTGAACTGCATGGATTTATGGGGAGAT
326 ATGTAAAAGGTTTGGTTATTGTGGATGTACACTCTCCCTTGAACTGCATGGATTTATGGGGAGAT
19247464 AACTACTTTCTTTATGTAAAAACATTGCTCACTAAGATATAGAATATTATCAAACTTTTTGGAAA
391 AACTACTTTCTTTATGTAAAAACATTGCTCACTAAGATATAGAATATTATCAAACTTTTTGGAAA
19247529 CACTCCCTACAAAGATCTTAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG-CGTAT
456 CACTCCCTACAAAGATCTTAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGCCGTAT
19247584 NTAGTGTTTACTGCTTTGCTTTCATCTTTTACAATTTCTCATTAGACTAGTGGAATGTTTACATA
1 -TAGTGTTTACTGCTTTGCTTTCATCTTTTACAATTTCTCATTAGACTAGTGGAATGTTTACATA
19247649 CATTTTTCATTAGACTAGTGTGCAATTTGTCTTGCATTTTGCACATTCCAGCCCAAACATGTGGG
65 CATTTTTCATTAGACTAGTGTGCAATTTGTCTTGCATTTTGCACATTCCAGCCCAAACATGTGGG
19247714 TTGTCTTTGGTAGTCCTGCAAAGTAAATGTCTCCGTTACAGTATTTATAGCTTTTGAAGTAATCA
130 TTGTCTTTGGTAGTCCTGCAAAGTAAATGTCTCCGTTACAGTATTTATAGCTTTTGAAGTAATCA
19247779 AATCATCACCTGGAGTTCAGGTGACAGATACAACTGGGTGTGCCACCACTCAAGAACCAATGATG
195 AATCATCACCTGGAGTTCAGGTGACAGATACAACTGGGTGTGCCACCACTCAAGAACCAATGATG
19247844 GGAGTCAGGTTTATGTCACTTTTATATATATGATGAGAGATATATGTGTAGTTACCTGTAAAAAT
260 GGAGTCAGGTTTATGTCACTTTTATATATATGATGAGAGATATATGTGTAGTTACCTGTAAAAAT
19247909 GATGTAAAAGGTTTGGTTATTGTGGATGTACACTCTCCCTTGAACTGCATGGATTTATGGGGAGA
325 GATGTAAAAGGTTTGGTTATTGTGGATGTACACTCTCCCTTGAACTGCATGGATTTATGGGGAGA
19247974 TAACTACTTTCTTTATGTAAAAACATTGCTCACTAAGATATAGAATATTATCAAACTTTTTGGAA
390 TAACTACTTTCTTTATGTAAAAACATTGCTCACTAAGATATAGAATATTATCAAACTTTTTGGAA
19248039 ACACTCCCTACAAAGATCTTAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGCCGTAT
455 ACACTCCCTACAAAGATCTTAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGCCGTAT
19248096 ATCTTTTGGT
Statistics
Matches: 510, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
511 505 0.99
512 5 0.01
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (511 bp):
TAGTGTTTACTGCTTTGCTTTCATCTTTTACAATTTCTCATTAGACTAGTGGAATGTTTACATAC
ATTTTTCATTAGACTAGTGTGCAATTTGTCTTGCATTTTGCACATTCCAGCCCAAACATGTGGGT
TGTCTTTGGTAGTCCTGCAAAGTAAATGTCTCCGTTACAGTATTTATAGCTTTTGAAGTAATCAA
ATCATCACCTGGAGTTCAGGTGACAGATACAACTGGGTGTGCCACCACTCAAGAACCAATGATGG
GAGTCAGGTTTATGTCACTTTTATATATATGATGAGAGATATATGTGTAGTTACCTGTAAAAATG
ATGTAAAAGGTTTGGTTATTGTGGATGTACACTCTCCCTTGAACTGCATGGATTTATGGGGAGAT
AACTACTTTCTTTATGTAAAAACATTGCTCACTAAGATATAGAATATTATCAAACTTTTTGGAAA
CACTCCCTACAAAGATCTTAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGCCGTAT
Found at i:19248067 original size:2 final size:2
Alignment explanation
Indices: 19248060--19248089 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
19248050 AAAGATCTTA
19248060 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
19248090 CCGTATATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:19259286 original size:48 final size:48
Alignment explanation
Indices: 19259230--19259325 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
19259220 TATCCTTTGA
19259230 TAGTCTATCCAAGTAAGATGATCATCATGGGTGTTATCTCGAAAATCT
1 TAGTCTATCCAAGTAAGATGATCATCATGGGTGTTATCTCGAAAATCT
19259278 TAGTCTATCCAAGTAAGATGATCATCATGGGTGTTATCTCGAAAATCT
1 TAGTCTATCCAAGTAAGATGATCATCATGGGTGTTATCTCGAAAATCT
19259326 AACATCTCCT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (48 bp):
TAGTCTATCCAAGTAAGATGATCATCATGGGTGTTATCTCGAAAATCT
Found at i:19266095 original size:22 final size:22
Alignment explanation
Indices: 19266070--19266130 Score: 61
Period size: 24 Copynumber: 2.7 Consensus size: 22
19266060 ATTGTTATGC
19266070 ACATGGAG-GTAACATGTTGTCA
1 ACATGGAGTGTAACAT-TTGTCA
* *
19266092 ACATGGCGTGTAACATTTGTTTGA
1 ACATGGAGTGTAACATTTG--TCA
*
19266116 ACATGGCGTGTAACA
1 ACATGGAGTGTAACA
19266131 AAATTTTTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 10 0.29
23 7 0.21
24 17 0.50
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (22 bp):
ACATGGAGTGTAACATTTGTCA
Found at i:19266331 original size:27 final size:27
Alignment explanation
Indices: 19266301--19266367 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 27
19266291 CTGTTCTTGA
* *
19266301 ACATGGTGGGTAGCAACATCGTTATGC
1 ACATGGTGGGTAGAAACATCGTTATAC
* *
19266328 ACATGGTGGGCAGAAACATTGTTATAC
1 ACATGGTGGGTAGAAACATCGTTATAC
*
19266355 ACAAGGTGGGTAG
1 ACATGGTGGGTAG
19266368 TAAAATGTTG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.30, C:0.15, G:0.31, T:0.24
Consensus pattern (27 bp):
ACATGGTGGGTAGAAACATCGTTATAC
Found at i:19266393 original size:23 final size:22
Alignment explanation
Indices: 19266367--19266444 Score: 66
Period size: 23 Copynumber: 3.4 Consensus size: 22
19266357 AAGGTGGGTA
*
19266367 GTAAAATGTTGTCAAAATGGCGT
1 GTAAAAT-TTGTCAACATGGCGT
* ** *
19266390 GTAACAATTTTTGGACATGACGT
1 GTAA-AATTTGTCAACATGGCGT
*
19266413 GTAACATATTGTCAACATGGCGT
1 GTAAAAT-TTGTCAACATGGCGT
*
19266436 GTAACATTT
1 GTAAAATTT
19266445 ATTTAAACAT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
22 4 0.09
23 36 0.84
24 3 0.07
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.33
Consensus pattern (22 bp):
GTAAAATTTGTCAACATGGCGT
Found at i:19269104 original size:13 final size:13
Alignment explanation
Indices: 19269086--19269115 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
19269076 TGTCATCATG
19269086 TTGTTATTCTAGC
1 TTGTTATTCTAGC
*
19269099 TTGTTATTCTAGT
1 TTGTTATTCTAGC
19269112 TTGT
1 TTGT
19269116 AACGGTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.13, C:0.10, G:0.17, T:0.60
Consensus pattern (13 bp):
TTGTTATTCTAGC
Found at i:19269484 original size:67 final size:67
Alignment explanation
Indices: 19269401--19269693 Score: 293
Period size: 67 Copynumber: 4.3 Consensus size: 67
19269391 CCATTTAAAA
* * * * * * *
19269401 AAGTCTTATATTGTTACACGCTAAGCTTGTTAGATCTCGTTAACATCCTGTGACATGCCTTTTTG
1 AAGTCTTATATTGTTACACGCCAAGCTTGATAGATGTCGTTGACATCTTGTGACATGCCATTTCG
19269466 TG
66 TG
* * * * * *
19269468 AAGTCTTATTTTGTTACATGCCACGCTTGATAGATGTCGTTGACATTTTGTGACACGCCATTTCA
1 AAGTCTTATATTGTTACACGCCAAGCTTGATAGATGTCGTTGACATCTTGTGACATGCCATTTCG
*
19269533 TA
66 TG
* * * * * *
19269535 AAGTCTTATATTGTTATACGCCATGCTTGATGGATGTCATTGACATCTTGTCACATGGCATTTCG
1 AAGTCTTATATTGTTACACGCCAAGCTTGATAGATGTCGTTGACATCTTGTGACATGCCATTTCG
19269600 TG
66 TG
* * * * *
19269602 AAGTCTTATATTGTTACACTCCACGCTTGGTAGATGTTGTTGACATTTTCTTGTGACATGCGATT
1 AAGTCTTATATTGTTACACGCCAAGCTTGATAGATGTCGTTGACA---TCTTGTGACATGCCATT
*
19269667 TTGTTG
63 TCG-TG
*
19269673 AAGTCTTCTA--GTTACACGCCA
1 AAGTCTTATATTGTTACACGCCA
19269694 TTTCGTTGAG
Statistics
Matches: 183, Mismatches: 39, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
67 146 0.80
69 10 0.05
70 16 0.09
71 11 0.06
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.40
Consensus pattern (67 bp):
AAGTCTTATATTGTTACACGCCAAGCTTGATAGATGTCGTTGACATCTTGTGACATGCCATTTCG
TG
Found at i:19269525 original size:134 final size:134
Alignment explanation
Indices: 19269381--19269650 Score: 353
Period size: 134 Copynumber: 2.0 Consensus size: 134
19269371 TAACATTTTC
* * * *
19269381 TTGTTACACGCCATTTAAAAAAGTCTTATATTGTTACACGCTAAGCTTGTTAGATCTCGTTAACA
1 TTGTGACACGCCATTTAAAAAAGTCTTATATTGTTACACGCCAAGCTTGATAGATCTCATTAACA
* * * *
19269446 TCCTGTGACATGCCTTTTTGTGAAGTCTTATTTTGTTACA-TGCCACGCTTGATAGATGTCGTTG
66 TCCTGTCACATGCCATTTCGTGAAGTCTTATATTGTTACACT-CCACGCTTGATAGATGTCGTTG
19269510 ACATT
130 ACATT
* * * * * * *
19269515 TTGTGACACGCCATTTCATAAAGTCTTATATTGTTATACGCCATGCTTGATGGATGTCATTGACA
1 TTGTGACACGCCATTTAAAAAAGTCTTATATTGTTACACGCCAAGCTTGATAGATCTCATTAACA
* * * *
19269580 TCTTGTCACATGGCATTTCGTGAAGTCTTATATTGTTACACTCCACGCTTGGTAGATGTTGTTGA
66 TCCTGTCACATGCCATTTCGTGAAGTCTTATATTGTTACACTCCACGCTTGATAGATGTCGTTGA
19269645 CATT
131 CATT
19269649 TT
1 TT
19269651 CTTGTGACAT
Statistics
Matches: 116, Mismatches: 19, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
134 115 0.99
135 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.40
Consensus pattern (134 bp):
TTGTGACACGCCATTTAAAAAAGTCTTATATTGTTACACGCCAAGCTTGATAGATCTCATTAACA
TCCTGTCACATGCCATTTCGTGAAGTCTTATATTGTTACACTCCACGCTTGATAGATGTCGTTGA
CATT
Found at i:19269845 original size:170 final size:167
Alignment explanation
Indices: 19269560--19269867 Score: 375
Period size: 170 Copynumber: 1.8 Consensus size: 167
19269550 ATACGCCATG
* * *
19269560 CTTGATGGATGTCATTGACATCTTGTCACATGGCATTTCGTGAAGTCTTATATTGTTACACTCCA
1 CTTGATAGATGTCATTGACATCTTGTCACATGCCATTTCGTGAAGTCTTATATTGTTACACGCCA
* * * * ** ** * * * *
19269625 CGCTTGGTAGATGTTGTTGACATTTTCTTGTGACATGCGATTTTGTTGAAGTCTTCTA-GTTACA
66 CCCTTGATAGATATTGTTGACATCTTCTAATGACACACCATTTCGTTGAAGTCTTATATGTCACA
19269689 CGCCATTTCGTTGAGTATTATATTATTACATATAACA
131 CGCCATTTCGTTGAGTATTATATTATTACATATAACA
* * * *
19269726 CTTGATAGATGTCGTTGACATTTTGTGCTTACATGCCATTTTGTTGAAGTCTTATATTGTTACAG
1 CTTGATAGATGTCATTGACATCTTGT-C--ACATGCCATTTCG-TGAAGTCTTATATTGTTACAC
* *
19269791 GCGACCCTTGATAGATATTGTTGACATCTTCTAATTACACACCATTTCGTTGAAGTCTTATATTG
62 GCCACCCTTGATAGATATTGTTGACATCTTCTAATGACACACCATTTCGTTGAAGTCTTATA-TG
19269856 TCACACGCCATT
126 TCACACGCCATT
19269868 CTTGGTAGAT
Statistics
Matches: 115, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
166 23 0.20
167 1 0.01
169 11 0.10
170 68 0.59
172 12 0.10
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.41
Consensus pattern (167 bp):
CTTGATAGATGTCATTGACATCTTGTCACATGCCATTTCGTGAAGTCTTATATTGTTACACGCCA
CCCTTGATAGATATTGTTGACATCTTCTAATGACACACCATTTCGTTGAAGTCTTATATGTCACA
CGCCATTTCGTTGAGTATTATATTATTACATATAACA
Found at i:19270252 original size:71 final size:71
Alignment explanation
Indices: 19269676--19270250 Score: 547
Period size: 71 Copynumber: 8.2 Consensus size: 71
19269666 TTTGTTGAAG
* * * *** ** *
19269676 TCTTCTAGTTACACGCCATTTCGTTG-AGTATTATATTATTACATATAACACTTGATAGATGTCG
1 TCTTCTTGTTACACGCCATTTCGTTGAAGTCTTATATTGTTACATGCCATTCTTGTTAGATGTCG
19269740 TTGACA
66 TTGACA
* * * * ** * *
19269746 T-TT-TGTGCTTACATGCCATTTTGTTGAAGTCTTATATTGTTACAGGCGACCCTTGATAGATAT
1 TCTTCT-TG-TTACACGCCATTTCGTTGAAGTCTTATATTGTTACATGCCATTCTTGTTAGATGT
*
19269809 TGTTGACA
64 CGTTGACA
** * * * * *
19269817 TCTTCTAATTACACACCATTTCGTTGAAGTCTTATATTGTCACACGCCATTCTTGGTAGATGTTG
1 TCTTCTTGTTACACGCCATTTCGTTGAAGTCTTATATTGTTACATGCCATTCTTGTTAGATGTCG
19269882 TTGACA
66 TTGACA
* * * * * *
19269888 TTTTCTTGTGACACGCTA-TTC-TTGAAGTCTTATATTGTTGCATGCTATTCTTGTTAGATGTAG
1 TCTTCTTGTTACACGCCATTTCGTTGAAGTCTTATATTGTTACATGCCATTCTTGTTAGATGTCG
19269951 TTGACA
66 TTGACA
* * * * * *
19269957 ---TCTTGTGACACACCATTTCGTTGAAGTCTTATACTATCACATGCCATTCTTGTTAGATGTCA
1 TCTTCTTGTTACACGCCATTTCGTTGAAGTCTTATATTGTTACATGCCATTCTTGTTAGATGTCG
19270019 TTGACA
66 TTGACA
* * * * * * *
19270025 TCTTCTTGTCACACGTCATTTCGTTGAAGTTTTATATTGTCACAAGCCATTCTAGTTAGATGTTG
1 TCTTCTTGTTACACGCCATTTCGTTGAAGTCTTATATTGTTACATGCCATTCTTGTTAGATGTCG
*
19270090 CTGACA
66 TTGACA
* * * * * * *
19270096 ACTTCTTGTCACACACCATTTCGTTTAAATCTTATATTGTTACACT-CGATTCTTATTAGATGTC
1 TCTTCTTGTTACACGCCATTTCGTTGAAGTCTTATATTGTTACA-TGCCATTCTTGTTAGATGTC
*
19270160 ATTGACA
65 GTTGACA
* * *
19270167 TCTTCTTGTCACATGCCATTTCGTTGAGGTCTTATATTGTTACATGCCATTCTTGTTAGATGTCG
1 TCTTCTTGTTACACGCCATTTCGTTGAAGTCTTATATTGTTACATGCCATTCTTGTTAGATGTCG
*
19270232 TTTACA
66 TTGACA
19270238 TCTTCTTGTTACA
1 TCTTCTTGTTACA
19270251 TGTCCTGGCT
Statistics
Matches: 412, Mismatches: 81, Indels: 23
0.80 0.16 0.04
Matches are distributed among these distances:
66 13 0.03
67 3 0.01
68 42 0.10
69 45 0.11
70 21 0.05
71 285 0.69
72 2 0.00
73 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (71 bp):
TCTTCTTGTTACACGCCATTTCGTTGAAGTCTTATATTGTTACATGCCATTCTTGTTAGATGTCG
TTGACA
Found at i:19270784 original size:2 final size:2
Alignment explanation
Indices: 19270777--19270810 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
19270767 ATCGATCAAG
19270777 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19270811 NTTACCAACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19270848 original size:2 final size:2
Alignment explanation
Indices: 19270841--19270876 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
19270831 TATCGATCAA
19270841 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19270877 TGTCTATAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19270851 original size:65 final size:64
Alignment explanation
Indices: 19270746--19270877 Score: 246
Period size: 65 Copynumber: 2.0 Consensus size: 64
19270736 AATACTAAAC
*
19270746 ATTACCAACTCATAGTGGCATATCGATCAAGTATATATATATATATATATATATATATATATAT
1 ATTACCAACTCATAGTGGCATATCGATCAAATATATATATATATATATATATATATATATATAT
19270810 ANTTACCAACTCATAGTGGCATATCGATCAAATATATATATATATATATATATATATATATATAT
1 A-TTACCAACTCATAGTGGCATATCGATCAAATATATATATATATATATATATATATATATATAT
19270875 ATT
1 ATT
19270878 GTCTATAACA
Statistics
Matches: 66, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
64 3 0.05
65 63 0.95
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.39
Consensus pattern (64 bp):
ATTACCAACTCATAGTGGCATATCGATCAAATATATATATATATATATATATATATATATATAT
Found at i:19272017 original size:39 final size:40
Alignment explanation
Indices: 19271939--19272042 Score: 122
Period size: 41 Copynumber: 2.6 Consensus size: 40
19271929 ATCCAGCTCA
* *
19271939 TGTGCATCCCCCCACATCGTGCACATAGCCGGAGTCATCG
1 TGTGCATCCCCCCACATCGTGCACATAGCCAGAGCCATCG
* *
19271979 TGTGCATCCCCCCCACATCGTGCACA-A-TCAGTGCCATCG
1 TGTGCAT-CCCCCCACATCGTGCACATAGCCAGAGCCATCG
* * *
19272018 TGTACATCCCCTCACATCATGCACA
1 TGTGCATCCCCCCACATCGTGCACA
19272043 CGGGCACTAT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
38 16 0.29
39 14 0.25
40 8 0.14
41 18 0.32
ACGTcount: A:0.22, C:0.39, G:0.17, T:0.21
Consensus pattern (40 bp):
TGTGCATCCCCCCACATCGTGCACATAGCCAGAGCCATCG
Found at i:19272158 original size:40 final size:40
Alignment explanation
Indices: 19272103--19272193 Score: 182
Period size: 40 Copynumber: 2.3 Consensus size: 40
19272093 CATCCCCTCA
19272103 CATCGTGCACACACGATTATAATCATCACACAATATCAAC
1 CATCGTGCACACACGATTATAATCATCACACAATATCAAC
19272143 CATCGTGCACACACGATTATAATCATCACACAATATCAAC
1 CATCGTGCACACACGATTATAATCATCACACAATATCAAC
19272183 CATCGTGCACA
1 CATCGTGCACA
19272194 ACATATATAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.38, C:0.31, G:0.09, T:0.22
Consensus pattern (40 bp):
CATCGTGCACACACGATTATAATCATCACACAATATCAAC
Found at i:19272169 original size:23 final size:23
Alignment explanation
Indices: 19272103--19272169 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
19272093 CATCCCCTCA
19272103 CATCGTGCACACACGATTATAAT
1 CATCGTGCACACACGATTATAAT
*
19272126 CA---T-CACACA--A-TATCAAC
1 CATCGTGCACACACGATTAT-AAT
19272143 CATCGTGCACACACGATTATAAT
1 CATCGTGCACACACGATTATAAT
19272166 CATC
1 CATC
19272170 ACACAATATC
Statistics
Matches: 34, Mismatches: 2, Indels: 16
0.65 0.04 0.31
Matches are distributed among these distances:
16 3 0.09
17 5 0.15
19 6 0.18
20 2 0.06
21 6 0.18
23 9 0.26
24 3 0.09
ACGTcount: A:0.37, C:0.30, G:0.09, T:0.24
Consensus pattern (23 bp):
CATCGTGCACACACGATTATAAT
Found at i:19287068 original size:23 final size:23
Alignment explanation
Indices: 19287014--19287068 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
19287004 GCTATACAGA
* * *
19287014 CCAAGTACA-ATGTTGTTACATG
1 CCAAGTATATATGTTCTTACACG
* *
19287036 CCATGCATATATGTTCTTACACG
1 CCAAGTATATATGTTCTTACACG
19287059 CCAAGTATAT
1 CCAAGTATAT
19287069 TTATTTATAT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 6 0.24
23 19 0.76
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.33
Consensus pattern (23 bp):
CCAAGTATATATGTTCTTACACG
Found at i:19287506 original size:23 final size:22
Alignment explanation
Indices: 19287454--19287654 Score: 143
Period size: 23 Copynumber: 8.8 Consensus size: 22
19287444 ATTTAAATTT
* *
19287454 ATGGCGTGTCACATATTCTTACA
1 ATGGCGTGTCACATATTCCT-CC
*
19287477 ATAGCGTGTCACATATTTCCTCC
1 ATGGCGTGTCACATA-TTCCTCC
* **
19287500 ATGGCGTGTCACAAAGAGCCTCC
1 ATGGCGTGTCACATA-TTCCTCC
* * *
19287523 ATGGCGTGCCACGTATTCTCACC
1 ATGGCGTGTCACATATTC-CTCC
* * **
19287546 ATTGCGTGTCACAAAGAGCCTCC
1 ATGGCGTGTCACATA-TTCCTCC
* *
19287569 ATGGCATGTCACATATTCTCACC
1 ATGGCGTGTCACATATTC-CTCC
* *
19287592 ATGGCATGTCACATATTCTCACC
1 ATGGCGTGTCACATATTC-CTCC
*
19287615 ATGACGTGTCACATATTTCCT-C
1 ATGGCGTGTCACATA-TTCCTCC
* *
19287637 ATGGCATCTCACATATTC
1 ATGGCGTGTCACATATTC
19287655 ATTATATGGT
Statistics
Matches: 140, Mismatches: 33, Indels: 12
0.76 0.18 0.06
Matches are distributed among these distances:
21 3 0.02
22 15 0.11
23 114 0.81
24 8 0.06
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.29
Consensus pattern (22 bp):
ATGGCGTGTCACATATTCCTCC
Found at i:19287530 original size:46 final size:46
Alignment explanation
Indices: 19287480--19287604 Score: 180
Period size: 46 Copynumber: 2.7 Consensus size: 46
19287470 TCTTACAATA
*
19287480 GCGTGTCACATATT-TCCTCCATGGCGTGTCACAAAGAGCCTCCATG
1 GCGTGTCACATATTCT-CACCATGGCGTGTCACAAAGAGCCTCCATG
* * *
19287526 GCGTGCCACGTATTCTCACCATTGCGTGTCACAAAGAGCCTCCATG
1 GCGTGTCACATATTCTCACCATGGCGTGTCACAAAGAGCCTCCATG
* *
19287572 GCATGTCACATATTCTCACCATGGCATGTCACA
1 GCGTGTCACATATTCTCACCATGGCGTGTCACA
19287605 TATTCTCACC
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
46 68 0.99
47 1 0.01
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (46 bp):
GCGTGTCACATATTCTCACCATGGCGTGTCACAAAGAGCCTCCATG
Found at i:19287672 original size:68 final size:68
Alignment explanation
Indices: 19287536--19287691 Score: 181
Period size: 68 Copynumber: 2.3 Consensus size: 68
19287526 GCGTGCCACG
* *
19287536 TATTCTCACCATTGCGTGTCACAAAGAGCCTCCATGGCATGTCACATATTCTCACCATGGCATGT
1 TATTCTCACCA-TGCGTGTCACAAAGAGCCTCCATGGCATCTCACATATTCTCACCATGGCATCT
19287601 CACA
65 CACA
* *** * * *
19287605 TATTCTCACCATGACGTGTCACATATTTCCT-CATGGCATCTCACATATTCATTA-TATGGTATC
1 TATTCTCACCATG-CGTGTCACAAAGAGCCTCCATGGCATCTCACATATTC-TCACCATGGCATC
19287668 TCACA
64 TCACA
19287673 TATTCTCACCATGGCGTGT
1 TATTCTCACCAT-GCGTGT
19287692 TACGTGGGAC
Statistics
Matches: 75, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
68 48 0.64
69 27 0.36
ACGTcount: A:0.25, C:0.28, G:0.14, T:0.33
Consensus pattern (68 bp):
TATTCTCACCATGCGTGTCACAAAGAGCCTCCATGGCATCTCACATATTCTCACCATGGCATCTC
ACA
Found at i:19287686 original size:23 final size:23
Alignment explanation
Indices: 19287567--19287687 Score: 140
Period size: 23 Copynumber: 5.3 Consensus size: 23
19287557 CAAAGAGCCT
19287567 CCATGGCATGTCACATATTCTCA
1 CCATGGCATGTCACATATTCTCA
19287590 CCATGGCATGTCACATATTCTCA
1 CCATGGCATGTCACATATTCTCA
* *
19287613 CCATGACGTGTCACATATT-TC-
1 CCATGGCATGTCACATATTCTCA
* *
19287634 CTCATGGCATCTCACATATTCATTA
1 C-CATGGCATGTCACATATTC-TCA
* * *
19287659 -TATGGTATCTCACATATTCTCA
1 CCATGGCATGTCACATATTCTCA
19287681 CCATGGC
1 CCATGGC
19287688 GTGTTACGTG
Statistics
Matches: 82, Mismatches: 11, Indels: 10
0.80 0.11 0.10
Matches are distributed among these distances:
21 1 0.01
22 19 0.23
23 61 0.74
24 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.12, T:0.33
Consensus pattern (23 bp):
CCATGGCATGTCACATATTCTCA
Found at i:19289342 original size:71 final size:71
Alignment explanation
Indices: 19289253--19289480 Score: 278
Period size: 71 Copynumber: 3.2 Consensus size: 71
19289243 ATTTGTGAAG
* * * * * *
19289253 AAAGTATTGATACTTATAAAGAAGGTATCGATATTTGTTGTCCAAAATGTCTTGGGAAGCATTCT
1 AAAGTATCGATACCTATAAGGAAGGTATTGATACTTGTTGTCCAAAATGTCTTGGGAAGCATTTT
19289318 GTTTGA
66 GTTTGA
* * *
19289324 AAAGTATCGATACCTATAAGGAAGGTATTGATACTTGTTGTCCAAAATGCCATGTGG-TGCATTT
1 AAAGTATCGATACCTATAAGGAAGGTATTGATACTTGTTGTCCAAAATGTCTTG-GGAAGCATTT
19289388 TGTTTGA
65 TGTTTGA
* * * * * *
19289395 AAAGTATCGATACCTAGAAGGAAGGTATTGATACTTGTTATCCAAAATGCTTTTAGAAAGTATTT
1 AAAGTATCGATACCTATAAGGAAGGTATTGATACTTGTTGTCCAAAATG-TCTTGGGAAGCATTT
*
19289460 TGTTTAA
65 TGTTTGA
*
19289467 AAAGTATTGATACC
1 AAAGTATCGATACC
19289481 CATGTCTTAA
Statistics
Matches: 134, Mismatches: 20, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
71 107 0.80
72 27 0.20
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.36
Consensus pattern (71 bp):
AAAGTATCGATACCTATAAGGAAGGTATTGATACTTGTTGTCCAAAATGTCTTGGGAAGCATTTT
GTTTGA
Found at i:19297403 original size:18 final size:18
Alignment explanation
Indices: 19297368--19297405 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
19297358 TGTTCTTGAA
*
19297368 AGCCTTAAATGCCTTTTT
1 AGCCTTAAAAGCCTTTTT
19297386 AGCCGTTAAAAGCCTTTTT
1 AGCC-TTAAAAGCCTTTTT
19297405 A
1 A
19297406 ATACTTGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.39
Consensus pattern (18 bp):
AGCCTTAAAAGCCTTTTT
Found at i:19317427 original size:13 final size:13
Alignment explanation
Indices: 19317409--19317433 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19317399 TTTCAGAAAA
19317409 TTTATAAAATCAT
1 TTTATAAAATCAT
19317422 TTTATAAAATCA
1 TTTATAAAATCA
19317434 CAATTTCTCC
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:19318313 original size:21 final size:22
Alignment explanation
Indices: 19318280--19318320 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
19318270 ACCTTTTTTT
* *
19318280 CACTTGTTTCCTTGAATTTTCA
1 CACTTGTTCCCTTAAATTTTCA
19318302 CACTT-TTCCCTTAAATTTT
1 CACTTGTTCCCTTAAATTTT
19318321 ACCCTTATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.20, C:0.24, G:0.05, T:0.51
Consensus pattern (22 bp):
CACTTGTTCCCTTAAATTTTCA
Found at i:19319475 original size:11 final size:11
Alignment explanation
Indices: 19319459--19319483 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
19319449 AGCTTTTGGG
19319459 TTTAAAGTTGT
1 TTTAAAGTTGT
19319470 TTTAAAGTTGT
1 TTTAAAGTTGT
19319481 TTT
1 TTT
19319484 GAAAAACTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.16, T:0.60
Consensus pattern (11 bp):
TTTAAAGTTGT
Found at i:19335592 original size:20 final size:20
Alignment explanation
Indices: 19335566--19335611 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
19335556 AATCTTACCC
* *
19335566 TTTTTCACTTGTTTCCTTGAA
1 TTTTACACTTG-TCCCTTGAA
19335587 TTTTCACACTTGTCCCTTGAA
1 TTTT-ACACTTGTCCCTTGAA
19335608 TTTT
1 TTTT
19335612 TCCACCTAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.15, C:0.22, G:0.09, T:0.54
Consensus pattern (20 bp):
TTTTACACTTGTCCCTTGAA
Found at i:19335613 original size:22 final size:22
Alignment explanation
Indices: 19335571--19335611 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
19335561 TACCCTTTTT
*
19335571 CACTTGTTTCCTTGAATTTTCA
1 CACTTGTTCCCTTGAATTTTCA
19335593 CACTTG-TCCCTTGAATTTT
1 CACTTGTTCCCTTGAATTTT
19335612 TCCACCTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.17, C:0.24, G:0.10, T:0.49
Consensus pattern (22 bp):
CACTTGTTCCCTTGAATTTTCA
Found at i:19338195 original size:37 final size:37
Alignment explanation
Indices: 19338154--19338231 Score: 131
Period size: 37 Copynumber: 2.1 Consensus size: 37
19338144 GTTGTGTGAG
19338154 GATGTT-GAAGTGTGCGAGTAGGGAGTGCACACATGAT
1 GATGTTAG-AGTGTGCGAGTAGGGAGTGCACACATGAT
*
19338191 GATGTTAGAGTGTGTGAGTAGGGAGTGCACACATGAT
1 GATGTTAGAGTGTGCGAGTAGGGAGTGCACACATGAT
19338228 GATG
1 GATG
19338232 AATGCATATG
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
37 38 0.97
38 1 0.03
ACGTcount: A:0.27, C:0.09, G:0.38, T:0.26
Consensus pattern (37 bp):
GATGTTAGAGTGTGCGAGTAGGGAGTGCACACATGAT
Found at i:19341937 original size:35 final size:35
Alignment explanation
Indices: 19341870--19341940 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 35
19341860 TTTCATTGGG
* *
19341870 CTTTTACAATGGCTTTTACCAGGCTCAGCCAAAAC
1 CTTTTACAATGGCTTTTACCAGGATCAACCAAAAC
*
19341905 CTTTTACAATGGTTTTTACC-GAGATCAACCAAAAC
1 CTTTTACAATGGCTTTTACCAG-GATCAACCAAAAC
19341940 C
1 C
19341941 CAACAACTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
34 1 0.03
35 31 0.97
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.30
Consensus pattern (35 bp):
CTTTTACAATGGCTTTTACCAGGATCAACCAAAAC
Found at i:19342598 original size:73 final size:73
Alignment explanation
Indices: 19342456--19342610 Score: 195
Period size: 73 Copynumber: 2.1 Consensus size: 73
19342446 CTTTTTTAGC
* * * * **
19342456 CGATTAAATTATTTCTGTCTTGAAGTCTAGATTTTTAGCAGTAGGCTCTTAGTCGACTAACTTAC
1 CGATTAAGTTAGTTCTGTCTTGAAGTCTAGATTTCTAGCAGTAGACTCTTAGTCGACTAACCCAC
19342521 TTCTTGGT
66 TTCTTGGT
* * *
19342529 CGATTAAGTTAGTTCTGTCTTGAAGT-TCAGATTTCTGGCAGTAGACTCTTAGTCGATTGACCCA
1 CGATTAAGTTAGTTCTGTCTTGAAGTCT-AGATTTCTAGCAGTAGACTCTTAGTCGACTAACCCA
*
19342593 TTTCTTGGT
65 CTTCTTGGT
*
19342602 CGACTAAGT
1 CGATTAAGT
19342611 CTTTTCTGTT
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
72 1 0.01
73 69 0.99
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40
Consensus pattern (73 bp):
CGATTAAGTTAGTTCTGTCTTGAAGTCTAGATTTCTAGCAGTAGACTCTTAGTCGACTAACCCAC
TTCTTGGT
Found at i:19343035 original size:21 final size:21
Alignment explanation
Indices: 19343006--19343048 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
19342996 GCAAAGTAGA
19343006 TTTTCTTATATT-TCATAAAC
1 TTTTCTTATATTATCATAAAC
*
19343026 TTTTACTTATCTTATCATAAAC
1 TTTT-CTTATATTATCATAAAC
19343048 T
1 T
19343049 CAAAATTAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 4 0.20
21 7 0.35
22 9 0.45
ACGTcount: A:0.30, C:0.16, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTTCTTATATTATCATAAAC
Found at i:19347007 original size:37 final size:37
Alignment explanation
Indices: 19346900--19347010 Score: 123
Period size: 37 Copynumber: 3.0 Consensus size: 37
19346890 NNNNNNCTCT
* ** * *
19346900 TGTGCACTCCCTACACGCACAAGGCAATACCACCATA
1 TGTGCACTCCCTACTCGCACAACTCAATATCATCATA
** * *
19346937 TGTGCACTCCCTACTCGCACATTTCAATGTCATCATG
1 TGTGCACTCCCTACTCGCACAACTCAATATCATCATA
* *
19346974 TGTGCACTCCCTACTCGCACACCTCATTATCATCATA
1 TGTGCACTCCCTACTCGCACAACTCAATATCATCATA
19347011 CAACATTATT
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.26, C:0.36, G:0.12, T:0.26
Consensus pattern (37 bp):
TGTGCACTCCCTACTCGCACAACTCAATATCATCATA
Found at i:19350309 original size:41 final size:42
Alignment explanation
Indices: 19350250--19350368 Score: 168
Period size: 41 Copynumber: 2.9 Consensus size: 42
19350240 CATCTCATAT
*
19350250 GCAACGGCTTATGCGCACTCCCACTCGCACATAGCCGAGTC-
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGAGTCA
* *
19350291 GCAACGGCTTATGTGCACTCCCACTCACACATAGCCGGGTCA
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGAGTCA
* * * *
19350333 GCAACGACTTATGTGCACTCCTAATTGCACATAGCC
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCC
19350369 AGGTCCACAT
Statistics
Matches: 69, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
41 38 0.55
42 31 0.45
ACGTcount: A:0.24, C:0.35, G:0.20, T:0.20
Consensus pattern (42 bp):
GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGAGTCA
Found at i:19353004 original size:205 final size:203
Alignment explanation
Indices: 19352652--19353059 Score: 753
Period size: 205 Copynumber: 2.0 Consensus size: 203
19352642 CCAAATCTTT
19352652 AAGGCAAACACAATTGCTGCCATATCCAAATCGTGTGCGGGGTAATTCTACTCATGCCTTTTAAG
1 AAGGCAAACACAATTGCTGCCATATCCAAATCGTGTGCGGGGTAATTCTACTCATGCCTTTTAAG
* * * * *
19352717 TTGCCTTGATGTATACGCAATCACCTTCCCATGCTGCATTAATACACACCCTAAACCAACCTGCA
66 ATGCCTGGATGCATACGCAATCACCCTCCCATGCTGCATTAATACACAACCTAAACCAACCTGCA
19352782 ATGCATCACAAAATACCGTATAACCCCCTTGTGCCTTGCGGTAGGCTTAATACTAAAGTTGTGGT
131 ATGCATCACAAAATACCGTATAA-CCCCTTGTGCCTTGCGGTAGGCTTAATACTAAAGTTGTGGT
19352847 GAGACATGC
195 GAGACATGC
19352856 NAAGGCAAACACAATTGCTGCCATATCCAAATCGTGTGCGGGGTAATTCTACTCATGCCTTTTAA
1 -AAGGCAAACACAATTGCTGCCATATCCAAATCGTGTGCGGGGTAATTCTACTCATGCCTTTTAA
19352921 GATGCCTGGATGCATACGCAATCACCCTCCCATGCTGCATTAATACACAACCTAAACCAACCTGC
65 GATGCCTGGATGCATACGCAATCACCCTCCCATGCTGCATTAATACACAACCTAAACCAACCTGC
19352986 AATGCATCACAAAATACCGTATAACCCCTTGTGCCTTGCGGTAGGCTTAATACTAAAGTTGTGGT
130 AATGCATCACAAAATACCGTATAACCCCTTGTGCCTTGCGGTAGGCTTAATACTAAAGTTGTGGT
19353051 GAGACATGC
195 GAGACATGC
19353060 CTTAAGCTTC
Statistics
Matches: 198, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
204 50 0.25
205 148 0.75
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.26
Consensus pattern (203 bp):
AAGGCAAACACAATTGCTGCCATATCCAAATCGTGTGCGGGGTAATTCTACTCATGCCTTTTAAG
ATGCCTGGATGCATACGCAATCACCCTCCCATGCTGCATTAATACACAACCTAAACCAACCTGCA
ATGCATCACAAAATACCGTATAACCCCTTGTGCCTTGCGGTAGGCTTAATACTAAAGTTGTGGTG
AGACATGC
Found at i:19356700 original size:22 final size:22
Alignment explanation
Indices: 19356675--19356716 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
19356665 AAACAGAATG
19356675 TTTCTCACTGCAGCAAGAACGC
1 TTTCTCACTGCAGCAAGAACGC
** *
19356697 TTTCTTGCTGCAGCGAGAAC
1 TTTCTCACTGCAGCAAGAAC
19356717 CAAGGCACCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (22 bp):
TTTCTCACTGCAGCAAGAACGC
Found at i:19357037 original size:37 final size:37
Alignment explanation
Indices: 19356930--19357040 Score: 123
Period size: 37 Copynumber: 3.0 Consensus size: 37
19356920 CCTCAGCTCT
* ** * *
19356930 TGTGCACTCCCTACACGCACAAGGCAATACCACCATA
1 TGTGCACTCCCTACTCGCACAACTCAATATCATCATA
** * *
19356967 TGTGCACTCCCTACTCGCACATTTCAATGTCATCATG
1 TGTGCACTCCCTACTCGCACAACTCAATATCATCATA
* *
19357004 TGTGCACTCCCTACTCGCACACCTCATTATCATCATA
1 TGTGCACTCCCTACTCGCACAACTCAATATCATCATA
19357041 CAACATTATT
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.26, C:0.36, G:0.12, T:0.26
Consensus pattern (37 bp):
TGTGCACTCCCTACTCGCACAACTCAATATCATCATA
Found at i:19358637 original size:22 final size:23
Alignment explanation
Indices: 19358605--19358660 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
19358595 AACTTCAAAG
* **
19358605 ATTAATTTTTAGATTTTTTTCTT
1 ATTATTTTTTAGATTCATTTCTT
19358628 A-TATTTTTTAGATTCATTTCTT
1 ATTATTTTTTAGATTCATTTCTT
*
19358650 ATTCTTTTTTA
1 ATTATTTTTTA
19358661 AAAAGATTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 19 0.68
23 9 0.32
ACGTcount: A:0.21, C:0.07, G:0.04, T:0.68
Consensus pattern (23 bp):
ATTATTTTTTAGATTCATTTCTT
Found at i:19359352 original size:26 final size:23
Alignment explanation
Indices: 19359318--19359383 Score: 71
Period size: 26 Copynumber: 2.7 Consensus size: 23
19359308 TTTTAATAAA
19359318 AGAATAAGAGAAAAAGAAAATGATGG
1 AGAA-AAGAGAAAAAGAAAA-GA-GG
*
19359344 AGTAAAAGAGAAATAGAAAAGAGG
1 AG-AAAAGAGAAAAAGAAAAGAGG
*
19359368 AGAACA-AGAAAAAGAA
1 AGAAAAGAGAAAAAGAA
19359384 CGATTGAAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
22 9 0.25
23 3 0.08
24 4 0.11
25 2 0.06
26 16 0.44
27 2 0.06
ACGTcount: A:0.65, C:0.02, G:0.26, T:0.08
Consensus pattern (23 bp):
AGAAAAGAGAAAAAGAAAAGAGG
Found at i:19362767 original size:126 final size:123
Alignment explanation
Indices: 19362511--19362745 Score: 274
Period size: 126 Copynumber: 1.8 Consensus size: 123
19362501 TGTTTAAAAG
* * * *
19362511 TGTTCAAAATTTCTTTTTATTAATCCAATAAGAGATTGCAAATATTAAAAAAAAAGAAAATGGAT
1 TGTTTAAAATTTCTTTTTATTAATCAAATAAAAGATTACAAATATTAAAAAAAAAGAAAATGGAT
* *
19362576 AAATTAAAAAAATGAAATAAATATTATTTTAAAAAATCAAAATAAAAAATTTGTTTATAAA
66 AAATAAAAAAAATAAAATAAATATTATTTTAAAAAATCAAAATAAAAAA--TG-TTATAAA
* *
19362637 TGTTTAAAA-TTCTCTTTTGTTAATCAAATAAAAGATTATAAATATTAAAGGAAAAAAAGAAAAT
1 TGTTTAAAATTTCT-TTTTATTAATCAAATAAAAGATTACAAATATT-AA--AAAAAAAGAAAAT
* *
19362701 GGGTTAAGTAAAAAAAGAGTAAAATAAATATTATTTTCAAAAAAT
62 -GGATAAATAAAAAAA-A-TAAAATAAATATTATTTT-AAAAAAT
19362746 TAAGATTAAA
Statistics
Matches: 91, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
125 4 0.04
126 35 0.38
127 2 0.02
129 13 0.14
130 12 0.13
131 1 0.01
132 17 0.19
133 7 0.08
ACGTcount: A:0.54, C:0.04, G:0.09, T:0.33
Consensus pattern (123 bp):
TGTTTAAAATTTCTTTTTATTAATCAAATAAAAGATTACAAATATTAAAAAAAAAGAAAATGGAT
AAATAAAAAAAATAAAATAAATATTATTTTAAAAAATCAAAATAAAAAATGTTATAAA
Found at i:19375399 original size:40 final size:41
Alignment explanation
Indices: 19375341--19375420 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 41
19375331 TTGTGAAAAA
*
19375341 CACCAATTGTGGCGAGGTTAG-AAACCCCACTAAAGTGAAC
1 CACCAATTGTGGCAAGGTTAGAAAACCCCACTAAAGTGAAC
*
19375381 CACCAATCT-TGGCAAGGTTAGAAAACCCCACTAAGGTGAA
1 CACCAAT-TGTGGCAAGGTTAGAAAACCCCACTAAAGTGAA
19375421 AAATAGCCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
40 18 0.50
41 18 0.50
ACGTcount: A:0.36, C:0.25, G:0.21, T:0.17
Consensus pattern (41 bp):
CACCAATTGTGGCAAGGTTAGAAAACCCCACTAAAGTGAAC
Found at i:19379217 original size:43 final size:42
Alignment explanation
Indices: 19379156--19379291 Score: 164
Period size: 43 Copynumber: 3.2 Consensus size: 42
19379146 TTGTGTGACA
* * *
19379156 ATGATGACCTCAGCTATGTGCGATGTGGGAGTGCACATGAGCTG
1 ATGATGACC-CAGCTATGTGCGA-GTGGGAGTGCGCATAAGCCG
* *
19379200 ATGATGACCCAGCTATGTGCGAGTAGGAGTGTGCATAAGCCG
1 ATGATGACCCAGCTATGTGCGAGTGGGAGTGCGCATAAGCCG
*** *
19379242 ATGATGACTTGGCTATGTGCAAGTAGGGAGTGCGCATAAGCCG
1 ATGATGACCCAGCTATGTGCGAGT-GGGAGTGCGCATAAGCCG
19379285 ATGATGA
1 ATGATGA
19379292 TGACCCGGCT
Statistics
Matches: 80, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
42 35 0.44
43 36 0.45
44 9 0.11
ACGTcount: A:0.26, C:0.17, G:0.34, T:0.24
Consensus pattern (42 bp):
ATGATGACCCAGCTATGTGCGAGTGGGAGTGCGCATAAGCCG
Found at i:19379245 original size:42 final size:42
Alignment explanation
Indices: 19379156--19379291 Score: 164
Period size: 42 Copynumber: 3.2 Consensus size: 42
19379146 TTGTGTGACA
* * * *
19379156 ATGATGACCTCAGCTATGTGCGATGTGGGAGTGCACATGAGCTG
1 ATGATGACC-CAGCTATGTGCGA-GTAGGAGTGCGCATAAGCCG
*
19379200 ATGATGACCCAGCTATGTGCGAGTAGGAGTGTGCATAAGCCG
1 ATGATGACCCAGCTATGTGCGAGTAGGAGTGCGCATAAGCCG
*** *
19379242 ATGATGACTTGGCTATGTGCAAGTAGGGAGTGCGCATAAGCCG
1 ATGATGACCCAGCTATGTGCGAGTA-GGAGTGCGCATAAGCCG
19379285 ATGATGA
1 ATGATGA
19379292 TGACCCGGCT
Statistics
Matches: 81, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
42 36 0.44
43 36 0.44
44 9 0.11
ACGTcount: A:0.26, C:0.17, G:0.34, T:0.24
Consensus pattern (42 bp):
ATGATGACCCAGCTATGTGCGAGTAGGAGTGCGCATAAGCCG
Found at i:19381032 original size:35 final size:35
Alignment explanation
Indices: 19380981--19381117 Score: 115
Period size: 35 Copynumber: 4.0 Consensus size: 35
19380971 TTTCACCAAG
* * *
19380981 CTTT-ACAATGGCTTTTATCAGGCTTAGCCAAAAC
1 CTTTCACAATGGTTTTTATCAGGCTCAACCAAAAC
* * *
19381015 CTTTCACAATGGTTTTTATCGGGATTAACCAAAAC
1 CTTTCACAATGGTTTTTATCAGGCTCAACCAAAAC
* * *
19381050 C---CA-AAGTGGTCTTTCA-AAGGCTCAACCACAAC
1 CTTTCACAA-TGGT-TTTTATCAGGCTCAACCAAAAC
* *
19381082 CTTTCACAATGGTTTTTAACGGGCTCAACCAAAAC
1 CTTTCACAATGGTTTTTATCAGGCTCAACCAAAAC
19381117 C
1 C
19381118 CAAAGTGGTT
Statistics
Matches: 81, Mismatches: 14, Indels: 15
0.74 0.13 0.14
Matches are distributed among these distances:
31 2 0.02
32 18 0.22
33 4 0.05
34 8 0.10
35 47 0.58
36 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (35 bp):
CTTTCACAATGGTTTTTATCAGGCTCAACCAAAAC
Found at i:19381091 original size:67 final size:66
Alignment explanation
Indices: 19381012--19381187 Score: 271
Period size: 67 Copynumber: 2.6 Consensus size: 66
19381002 GCTTAGCCAA
19381012 AACCTTTCACAATGGTTTTTATCGGGATTAACCAAAACCCAAAGTGGTCTTTCAAAGGCTCAACC
1 AACCTTTCACAATGGTTTTTA-CGGGATTAACCAAAACCCAAAGTGGTCTTTCAAAGGCTCAACC
19381077 AC
65 AC
* * *
19381079 AACCTTTCACAATGGTTTTTAACGGGCTCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
1 AACCTTTCACAATGGTTTTT-ACGGGATTAACCAAAACCCAAAGTGGTCTTTCAAAGGCTCAACC
19381144 AC
65 AC
* * *
19381146 AATCTATAACAATGGTTTTTCACGGGATTAACCAAAACCCAA
1 AACCTTTCACAATGGTTTTT-ACGGGATTAACCAAAACCCAA
19381188 CAACTAACTT
Statistics
Matches: 99, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
67 98 0.99
68 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.26
Consensus pattern (66 bp):
AACCTTTCACAATGGTTTTTACGGGATTAACCAAAACCCAAAGTGGTCTTTCAAAGGCTCAACCA
C
Found at i:19381139 original size:32 final size:32
Alignment explanation
Indices: 19381041--19381144 Score: 122
Period size: 32 Copynumber: 3.2 Consensus size: 32
19381031 TATCGGGATT
*
19381041 AACCAAAACCCAAAGTGGTCTTTCAAAGGCTC
1 AACCAAAACCCAAAGTGGTTTTTCAAAGGCTC
* *
19381073 AACCACAACCTTTCACAA-TGGTTTTT-AACGGGCTC
1 AACCAAAACC---CA-AAGTGGTTTTTCAA-AGGCTC
19381108 AACCAAAACCCAAAGTGGTTTTTCAAAGGCTC
1 AACCAAAACCCAAAGTGGTTTTTCAAAGGCTC
19381140 AACCA
1 AACCA
19381145 CAATCTATAA
Statistics
Matches: 60, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
31 2 0.03
32 29 0.48
33 2 0.03
34 2 0.03
35 23 0.38
36 2 0.03
ACGTcount: A:0.36, C:0.28, G:0.14, T:0.22
Consensus pattern (32 bp):
AACCAAAACCCAAAGTGGTTTTTCAAAGGCTC
Found at i:19381167 original size:35 final size:35
Alignment explanation
Indices: 19381056--19381167 Score: 106
Period size: 35 Copynumber: 3.3 Consensus size: 35
19381046 AAACCCAAAG
* * * *
19381056 TGGTCTTTCAAAGGCTCAACCACAACCTTTCACAA
1 TGGTTTTTCAAAGGCTCAACCACAAACTATAACAA
* ** *
19381091 TGGTTTTT-AACGGGCTCAACCA-AAAC-CCAA-AG
1 TGGTTTTTCAA-AGGCTCAACCACAAACTATAACAA
*
19381123 TGGTTTTTCAAAGGCTCAACCACAATCTATAACAA
1 TGGTTTTTCAAAGGCTCAACCACAAACTATAACAA
19381158 TGGTTTTTCA
1 TGGTTTTTCA
19381168 CGGGATTAAC
Statistics
Matches: 60, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
32 19 0.32
33 6 0.10
34 7 0.12
35 28 0.47
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (35 bp):
TGGTTTTTCAAAGGCTCAACCACAAACTATAACAA
Found at i:19381672 original size:73 final size:73
Alignment explanation
Indices: 19381575--19381756 Score: 226
Period size: 73 Copynumber: 2.5 Consensus size: 73
19381565 GACAGAATGA
*
19381575 TCTTAGTCGACTAACTGTCC-TCTTAGTCGACTAAGTTGTCTTTGTCTTCTAAACCCAG-TTTTT
1 TCTTAGTCGACTAACT-TCCTTCTTAGTCGACTAAGTTGTCTTTGTCTT-TAAACCCAGATTTAT
*
19381638 GGCAGT-GAAC
64 GGCAATAG-AC
* * **
19381648 TCTTAGTCGACTAACTTCCTTCTTAGTCGATTAAGTTGTTTTTGTCTTTAAGTCCAGATTTATGG
1 TCTTAGTCGACTAACTTCCTTCTTAGTCGACTAAGTTGTCTTTGTCTTTAAACCCAGATTTATGG
*
19381713 CAATAGGC
66 CAATAGAC
* * *
19381721 TTTTAGTCGACTAACTTACTTCTTGGTCGACTAAGT
1 TCTTAGTCGACTAACTTCCTTCTTAGTCGACTAAGT
19381757 CTTCTCTGTC
Statistics
Matches: 95, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
72 10 0.11
73 84 0.88
74 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.41
Consensus pattern (73 bp):
TCTTAGTCGACTAACTTCCTTCTTAGTCGACTAAGTTGTCTTTGTCTTTAAACCCAGATTTATGG
CAATAGAC
Found at i:19384762 original size:19 final size:20
Alignment explanation
Indices: 19384738--19384783 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
19384728 GAAATTCAAT
*
19384738 TTAAAGAAT-TTTTAATTGG
1 TTAAAGAATATTTTAATTGA
*
19384757 TTAAAGTATATTTTAATTGA
1 TTAAAGAATATTTTAATTGA
19384777 TTAAAGA
1 TTAAAGA
19384784 TGAAGGGGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (20 bp):
TTAAAGAATATTTTAATTGA
Found at i:19387076 original size:27 final size:26
Alignment explanation
Indices: 19387019--19387078 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
19387009 GGCTGGCCAT
* * *
19387019 AAGGAAAGAACAAGAGAGAAAATAGA
1 AAGGAAAGAACAAAAGAGAAAAAACA
* *
19387045 GAGGAAAGGAAGAAAAGAGAAAAAACA
1 AAGGAAA-GAACAAAAGAGAAAAAACA
19387072 AAGGAAA
1 AAGGAAA
19387079 ACTAGAAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 6 0.22
27 21 0.78
ACGTcount: A:0.67, C:0.03, G:0.28, T:0.02
Consensus pattern (26 bp):
AAGGAAAGAACAAAAGAGAAAAAACA
Found at i:19393037 original size:19 final size:20
Alignment explanation
Indices: 19393003--19393042 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
19392993 TTCTGGGGTT
19393003 TTAAAATTCTCAATTTCATC
1 TTAAAATTCTCAATTTCATC
* *
19393023 TTAAAA-TCTCTATTTGATC
1 TTAAAATTCTCAATTTCATC
19393042 T
1 T
19393043 AGTTCGAGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.33, C:0.17, G:0.03, T:0.47
Consensus pattern (20 bp):
TTAAAATTCTCAATTTCATC
Found at i:19395527 original size:2 final size:2
Alignment explanation
Indices: 19395520--19395570 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
19395510 TTAGGTGCTT
*
19395520 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AT AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
19395562 AG AG AG AG A
1 AG AG AG AG A
19395571 ACTCCCATAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.47, T:0.02
Consensus pattern (2 bp):
AG
Found at i:19396227 original size:42 final size:42
Alignment explanation
Indices: 19396175--19396327 Score: 180
Period size: 42 Copynumber: 3.6 Consensus size: 42
19396165 GTAATGATAT
*
19396175 TGACCCGGCTATGTGCGAGTAGGAGTGTGCATAAGCTGATGC
1 TGACTCGGCTATGTGCGAGTAGGAGTGTGCATAAGCTGATGC
* * * *
19396217 TTACTCGGCTACGTGTGAGTGGGAGTGTGCATAAGCTGATGC
1 TGACTCGGCTATGTGCGAGTAGGAGTGTGCATAAGCTGATGC
* * * *
19396259 TGACTTGGCTATGTGCGAGTAAGAGTGCGCATAAGCCGATGC
1 TGACTCGGCTATGTGCGAGTAGGAGTGTGCATAAGCTGATGC
* * * * *
19396301 TGACCCAGCCATGTGCTAGTGGGAGTG
1 TGACTCGGCTATGTGCGAGTAGGAGTG
19396328 CATATGAGCT
Statistics
Matches: 91, Mismatches: 20, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 91 1.00
ACGTcount: A:0.21, C:0.19, G:0.35, T:0.25
Consensus pattern (42 bp):
TGACTCGGCTATGTGCGAGTAGGAGTGTGCATAAGCTGATGC
Found at i:19396338 original size:84 final size:83
Alignment explanation
Indices: 19396181--19396341 Score: 200
Period size: 84 Copynumber: 1.9 Consensus size: 83
19396171 ATATTGACCC
* * * * * * *
19396181 GGCTATGTGCGAGTAGGAGTGTGCATAAGCTGATGCTTACTCGGCTACGTGTGAGTGGGAGTGTG
1 GGCTATGTGCGAGTAAGAGTGCGCATAAGCCGATGCTGACCCAGCCACGTGTGAGTGGGAG-GTG
19396246 CATAAGCTGATGCTGACTT
65 CATAAGCTGATGCTGACTT
*
19396265 GGCTATGTGCGAGTAAGAGTGCGCATAAGCCGATGCTGACCCAGCCATGTGCT-AGTGGGA-GTG
1 GGCTATGTGCGAGTAAGAGTGCGCATAAGCCGATGCTGACCCAGCCACGTG-TGAGTGGGAGGTG
19396328 CATATGAGCTGATG
65 CATA--AGCTGATG
19396342 ATGATGGGAG
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
82 7 0.11
84 58 0.88
85 1 0.02
ACGTcount: A:0.22, C:0.17, G:0.35, T:0.25
Consensus pattern (83 bp):
GGCTATGTGCGAGTAAGAGTGCGCATAAGCCGATGCTGACCCAGCCACGTGTGAGTGGGAGGTGC
ATAAGCTGATGCTGACTT
Found at i:19402122 original size:68 final size:65
Alignment explanation
Indices: 19401991--19402137 Score: 249
Period size: 68 Copynumber: 2.2 Consensus size: 65
19401981 ATATGGTAGT
*
19401991 CTAGGATTGACTATGGGAGTCTTGAAGTTGATGGACCAAATTTACCCCTGCTCCCATTGCATTGC
1 CTAGGATTGACTATGGGAGGCTTGAAGTTGATGGACCAAATTTACCCCTGCTCCCATTGCATTGC
*
19402056 CTAGGATTGACTATGGGAGGCTTGAAGTTGATCTTGGACCAAATTTACCCCTGCTCCCATTTCAT
1 CTAGGATTGACTATGGGAGGCTTGAAGTTGA---TGGACCAAATTTACCCCTGCTCCCATTGCAT
19402121 TGC
63 TGC
19402124 CTAGGATTGACTAT
1 CTAGGATTGACTAT
19402138 AAGGGCTCTA
Statistics
Matches: 77, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
65 30 0.39
68 47 0.61
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.32
Consensus pattern (65 bp):
CTAGGATTGACTATGGGAGGCTTGAAGTTGATGGACCAAATTTACCCCTGCTCCCATTGCATTGC
Found at i:19402153 original size:68 final size:68
Alignment explanation
Indices: 19401991--19402158 Score: 229
Period size: 68 Copynumber: 2.5 Consensus size: 68
19401981 ATATGGTAGT
** *
19401991 CTAGGATTGACTATGGGAGTCTTGAAGTTGA---TGGACCAAATTTACCCCTGCTCCCATTGCAT
1 CTAGGATTGACTATAAGAGGCTTGAAGTTGATCTTGGACCAAATTTACCCCTGCTCCCATTGCAT
19402053 TGC
66 TGC
** *
19402056 CTAGGATTGACTATGGGAGGCTTGAAGTTGATCTTGGACCAAATTTACCCCTGCTCCCATTTCAT
1 CTAGGATTGACTATAAGAGGCTTGAAGTTGATCTTGGACCAAATTTACCCCTGCTCCCATTGCAT
19402121 TGC
66 TGC
19402124 CTAGGATTGACTATAAG-GGCTCT-AGAGTTGATCTT
1 CTAGGATTGACTATAAGAGGCT-TGA-AGTTGATCTT
19402159 CAGCCACTAC
Statistics
Matches: 94, Mismatches: 4, Indels: 7
0.90 0.04 0.07
Matches are distributed among these distances:
65 30 0.32
67 5 0.05
68 59 0.63
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.32
Consensus pattern (68 bp):
CTAGGATTGACTATAAGAGGCTTGAAGTTGATCTTGGACCAAATTTACCCCTGCTCCCATTGCAT
TGC
Found at i:19405027 original size:63 final size:63
Alignment explanation
Indices: 19404920--19405038 Score: 175
Period size: 63 Copynumber: 1.9 Consensus size: 63
19404910 GAAATTGATG
* *
19404920 CAACCATGCATGTGCGGATTGGGAAGTGCAATGCCAGTTGAATGACAAAGGATGTGATAATTA
1 CAACCATGCATGTGCAGAGTGGGAAGTGCAATGCCAGTTGAATGACAAAGGATGTGATAATTA
* * * * *
19404983 CAACCGTGCATGTGCAGAGTGGGAAGTGCAATGCCGGTTTAATGATAAAGGTTGTG
1 CAACCATGCATGTGCAGAGTGGGAAGTGCAATGCCAGTTGAATGACAAAGGATGTG
19405039 GGGACGGCGA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
63 49 1.00
ACGTcount: A:0.30, C:0.14, G:0.31, T:0.24
Consensus pattern (63 bp):
CAACCATGCATGTGCAGAGTGGGAAGTGCAATGCCAGTTGAATGACAAAGGATGTGATAATTA
Found at i:19410312 original size:63 final size:63
Alignment explanation
Indices: 19410205--19410323 Score: 175
Period size: 63 Copynumber: 1.9 Consensus size: 63
19410195 GAAATTGATG
* *
19410205 CAACCATGCATGTGCGGATTGGGAAGTGCAATGCCAGTTGAATGACAAAGGATGTGATAATTA
1 CAACCATGCATGTGCAGAGTGGGAAGTGCAATGCCAGTTGAATGACAAAGGATGTGATAATTA
* * * * *
19410268 CAACCGTGCATGTGCAGAGTGGGAAGTGCAATGCCGGTTTAATGATAAAGGTTGTG
1 CAACCATGCATGTGCAGAGTGGGAAGTGCAATGCCAGTTGAATGACAAAGGATGTG
19410324 GGGACGACGA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
63 49 1.00
ACGTcount: A:0.30, C:0.14, G:0.31, T:0.24
Consensus pattern (63 bp):
CAACCATGCATGTGCAGAGTGGGAAGTGCAATGCCAGTTGAATGACAAAGGATGTGATAATTA
Found at i:19416993 original size:36 final size:36
Alignment explanation
Indices: 19416946--19417018 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
19416936 GCTTACATCT
*
19416946 ATGTTTTATGCTAAATGTTTAAATCTATTTGATTAA
1 ATGTTTTATGCTAAATGTTTAAATCTATGTGATTAA
* *
19416982 ATGTTTTATGCTGAATGTTTATATCTATGTGATTAA
1 ATGTTTTATGCTAAATGTTTAAATCTATGTGATTAA
19417018 A
1 A
19417019 AGTCAATCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.32, C:0.05, G:0.14, T:0.49
Consensus pattern (36 bp):
ATGTTTTATGCTAAATGTTTAAATCTATGTGATTAA
Found at i:19433243 original size:28 final size:28
Alignment explanation
Indices: 19433210--19433444 Score: 229
Period size: 28 Copynumber: 7.9 Consensus size: 28
19433200 GATAACTTTT
19433210 ACATGTTTGTCTTAATTTAGACAAGAAA
1 ACATGTTTGTCTTAATTTAGACAAGAAA
*
19433238 ACATGTTTGCCTTAATTTAGACAAGAAA
1 ACATGTTTGTCTTAATTTAGACAAGAAA
*
19433266 ACATGAAAACATATTTTTCTTAATTTAGACAAGAAA
1 ACATG--------TTTGTCTTAATTTAGACAAGAAA
19433302 ACATGTTTTGTCTTAATTTAGACAAGAAAA
1 ACATG-TTTGTCTTAATTTAGACAAG-AAA
* *
19433332 ACATGTATGTCTCAATTTAGGACAAGAAA
1 ACATGTTTGTCTTAATTTA-GACAAGAAA
* * *
19433361 A-ATATGTTGTCTTAATCTAGATAAGAAA
1 ACATGT-TTGTCTTAATTTAGACAAGAAA
* * *
19433389 ACATGTTTGTCTTAATTTAAAGAAGATA
1 ACATGTTTGTCTTAATTTAGACAAGAAA
* *
19433417 ACATATTTTGTCTTAATTAAAGACAAGA
1 ACAT-GTTTGTCTTAATT-TAGACAAGA
19433445 GTTGTCTTAA
Statistics
Matches: 172, Mismatches: 21, Indels: 26
0.79 0.10 0.12
Matches are distributed among these distances:
28 66 0.38
29 60 0.35
30 20 0.12
36 26 0.15
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (28 bp):
ACATGTTTGTCTTAATTTAGACAAGAAA
Found at i:19433288 original size:36 final size:36
Alignment explanation
Indices: 19433234--19433306 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
19433224 ATTTAGACAA
*
19433234 GAAAACATGTTTGCCTTAATTTAGACAAGAAAACAT
1 GAAAACATATTTGCCTTAATTTAGACAAGAAAACAT
**
19433270 GAAAACATATTTTTCTTAATTTAGACAAGAAAACAT
1 GAAAACATATTTGCCTTAATTTAGACAAGAAAACAT
19433306 G
1 G
19433307 TTTTGTCTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.30
Consensus pattern (36 bp):
GAAAACATATTTGCCTTAATTTAGACAAGAAAACAT
Found at i:19433323 original size:29 final size:29
Alignment explanation
Indices: 19433270--19433444 Score: 187
Period size: 29 Copynumber: 6.1 Consensus size: 29
19433260 AAGAAAACAT
19433270 GAAAACATATTTT-TCTTAATTTAGACAA
1 GAAAACATATTTTGTCTTAATTTAGACAA
*
19433298 GAAAACATGTTTTGTCTTAATTTAGACAA
1 GAAAACATATTTTGTCTTAATTTAGACAA
* * *
19433327 GAAAAACAT-GTATGTCTCAATTTAGGACAA
1 G-AAAACATATTTTGTCTTAATTTA-GACAA
* * *
19433357 GAAAA-ATATGTTGTCTTAATCTAGATAA
1 GAAAACATATTTTGTCTTAATTTAGACAA
* * *
19433385 GAAAACAT-GTTTGTCTTAATTTAAAGAA
1 GAAAACATATTTTGTCTTAATTTAGACAA
* *
19433413 GATAACATATTTTGTCTTAATTAAAGACAA
1 GAAAACATATTTTGTCTTAATT-TAGACAA
19433443 GA
1 GA
19433445 GTTGTCTTAA
Statistics
Matches: 120, Mismatches: 20, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
28 45 0.38
29 56 0.47
30 19 0.16
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (29 bp):
GAAAACATATTTTGTCTTAATTTAGACAA
Found at i:19433371 original size:58 final size:57
Alignment explanation
Indices: 19433287--19433444 Score: 183
Period size: 57 Copynumber: 2.7 Consensus size: 57
19433277 TATTTTTCTT
*
19433287 AATTTAGACAAGAAAACATGTTTTGTCTTAATTTAGACAAGAAAAACATGTATGTCTC
1 AATTTAGACAAGAAAA-ATATTTTGTCTTAATTTAGACAAGAAAAACATGTATGTCTC
* * * * *
19433345 AATTTAGGACAAGAAAAATATGTTGTCTTAATCTAGATAAG-AAAACATGTTTGTCTT
1 AATTTA-GACAAGAAAAATATTTTGTCTTAATTTAGACAAGAAAAACATGTATGTCTC
* * * *
19433402 AATTTAAAGAAGATAACATATTTTGTCTTAATTAAAGACAAGA
1 AATTTAGACAAGA-AAAATATTTTGTCTTAATT-TAGACAAGA
19433445 GTTGTCTTAA
Statistics
Matches: 83, Mismatches: 13, Indels: 7
0.81 0.13 0.07
Matches are distributed among these distances:
56 5 0.06
57 36 0.43
58 32 0.39
59 10 0.12
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (57 bp):
AATTTAGACAAGAAAAATATTTTGTCTTAATTTAGACAAGAAAAACATGTATGTCTC
Found at i:19436981 original size:37 final size:37
Alignment explanation
Indices: 19436931--19437008 Score: 131
Period size: 37 Copynumber: 2.1 Consensus size: 37
19436921 CATATGCATT
*
19436931 CATCATCATGTGTGCACTCTCTACTCGCACAC-TCTAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTTC-AA
19436968 CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
19437005 CATC
1 CATC
19437009 CTCACACAAC
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
37 37 0.95
38 2 0.05
ACGTcount: A:0.24, C:0.37, G:0.10, T:0.28
Consensus pattern (37 bp):
CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
Found at i:19438487 original size:39 final size:39
Alignment explanation
Indices: 19438444--19438560 Score: 120
Period size: 39 Copynumber: 3.1 Consensus size: 39
19438434 CACACACTGA
19438444 TGATATATGCCATGTGCAGTGTGGAAGTGCACATGACAG
1 TGATATATGCCATGTGCAGTGTGGAAGTGCACATGACAG
* * ** * *
19438483 TGATA-GTG--GTGTGTTGTGT-G-AGTGCACA-CACTG
1 TGATATATGCCATGTGCAGTGTGGAAGTGCACATGACAG
*
19438516 ATGATATATGCCATGTGCAGTGTGGAAGTGCACATGACGG
1 -TGATATATGCCATGTGCAGTGTGGAAGTGCACATGACAG
19438556 TGATA
1 TGATA
19438561 GTGGTGTGTT
Statistics
Matches: 59, Mismatches: 12, Indels: 14
0.69 0.14 0.16
Matches are distributed among these distances:
33 3 0.05
34 13 0.22
35 3 0.05
36 8 0.14
37 8 0.14
38 3 0.05
39 18 0.31
40 3 0.05
ACGTcount: A:0.26, C:0.14, G:0.32, T:0.28
Consensus pattern (39 bp):
TGATATATGCCATGTGCAGTGTGGAAGTGCACATGACAG
Found at i:19438502 original size:73 final size:73
Alignment explanation
Indices: 19438383--19438600 Score: 400
Period size: 73 Copynumber: 3.0 Consensus size: 73
19438373 CAACCGTGCG
* * *
19438383 TGTGCGGTGTGGGAGTGCACATGACGGTGATAGTGGTGTGCTGTGTGAGTGCACACACTGATGAT
1 TGTGCAGTGTGGAAGTGCACATGACGGTGATAGTGGTGTGTTGTGTGAGTGCACACACTGATGAT
19438448 ATATGCCA
66 ATATGCCA
*
19438456 TGTGCAGTGTGGAAGTGCACATGACAGTGATAGTGGTGTGTTGTGTGAGTGCACACACTGATGAT
1 TGTGCAGTGTGGAAGTGCACATGACGGTGATAGTGGTGTGTTGTGTGAGTGCACACACTGATGAT
19438521 ATATGCCA
66 ATATGCCA
19438529 TGTGCAGTGTGGAAGTGCACATGACGGTGATAGTGGTGTGTTGTGTGAGTGCACACACTGATGAT
1 TGTGCAGTGTGGAAGTGCACATGACGGTGATAGTGGTGTGTTGTGTGAGTGCACACACTGATGAT
19438594 ATATGCC
66 ATATGCC
19438601 TTATACGGCG
Statistics
Matches: 140, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 140 1.00
ACGTcount: A:0.22, C:0.14, G:0.35, T:0.28
Consensus pattern (73 bp):
TGTGCAGTGTGGAAGTGCACATGACGGTGATAGTGGTGTGTTGTGTGAGTGCACACACTGATGAT
ATATGCCA
Found at i:19443392 original size:55 final size:55
Alignment explanation
Indices: 19443301--19443674 Score: 558
Period size: 55 Copynumber: 6.8 Consensus size: 55
19443291 AACCACCGGC
* * *
19443301 TCATTAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCATCATCCACTAG
1 TCATCAGCTCATGTGCACTCCCACACCGCACATAGCTAGAATCATCATCCACTGG
* ** *
19443356 TCATCAACTCATGTGCACTCCCACACTACACATAGCTAGAATCATTATCCACCT-G
1 TCATCAGCTCATGTGCACTCCCACACCGCACATAGCTAGAATCATCATCCA-CTGG
* * *
19443411 TCATCAGCTTATGTGCACTCCCACACCGTACATAGCT-GAAATCATCATCCACCGG
1 TCATCAGCTCATGTGCACTCCCACACCGCACATAGCTAG-AATCATCATCCACTGG
* *
19443466 TCATCAGCTCATGTGCACTCCCACACCGCACATAGCTAAAATCATCATCCACCGG
1 TCATCAGCTCATGTGCACTCCCACACCGCACATAGCTAGAATCATCATCCACTGG
19443521 TCATCAGCTCATGTGCACTCCCACACCGCACATAGCTAGAATCATCATCCA-TCGG
1 TCATCAGCTCATGTGCACTCCCACACCGCACATAGCTAGAATCATCATCCACT-GG
19443576 TCATCAGCTCATGTGCACTCCCACACCGCACATAGCTAGAATCATCATCCA-TCGG
1 TCATCAGCTCATGTGCACTCCCACACCGCACATAGCTAGAATCATCATCCACT-GG
* *
19443631 TCATCAGCTCATGTGCACTCCCACACCGCACATAGTTGGAATCA
1 TCATCAGCTCATGTGCACTCCCACACCGCACATAGCTAGAATCA
19443675 CCCGTCATCA
Statistics
Matches: 294, Mismatches: 20, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
54 2 0.01
55 290 0.99
56 2 0.01
ACGTcount: A:0.28, C:0.36, G:0.14, T:0.23
Consensus pattern (55 bp):
TCATCAGCTCATGTGCACTCCCACACCGCACATAGCTAGAATCATCATCCACTGG
Found at i:19443489 original size:27 final size:27
Alignment explanation
Indices: 19443459--19443544 Score: 70
Period size: 27 Copynumber: 3.1 Consensus size: 27
19443449 AAATCATCAT
19443459 CCACCGGTCATCAGCTCATGTGCACTCC
1 CCACCGGTCATCAGCTCATGTGCACT-C
** * **
19443487 CACACCGCACAT-AGCTAAAAT-CA-TC
1 C-CACCGGTCATCAGCTCATGTGCACTC
19443512 ATCCACCGGTCATCAGCTCATGTGCACTC
1 --CCACCGGTCATCAGCTCATGTGCACTC
19443541 CCAC
1 CCAC
19443545 ACCGCACATA
Statistics
Matches: 42, Mismatches: 10, Indels: 13
0.65 0.15 0.20
Matches are distributed among these distances:
25 1 0.02
26 9 0.21
27 13 0.31
28 9 0.21
29 10 0.24
ACGTcount: A:0.26, C:0.41, G:0.14, T:0.20
Consensus pattern (27 bp):
CCACCGGTCATCAGCTCATGTGCACTC
Found at i:19445282 original size:39 final size:39
Alignment explanation
Indices: 19445228--19445316 Score: 160
Period size: 39 Copynumber: 2.3 Consensus size: 39
19445218 TGAGATTCAA
*
19445228 TCTCGCTGCAGCGAAATTGTAACCTAGAAACAAAAAGTT
1 TCTCGCTGCAGCGAAATTGCAACCTAGAAACAAAAAGTT
*
19445267 TCTCGCTGCAGCGAAATTGCAACCTAGAAACAGAAAGTT
1 TCTCGCTGCAGCGAAATTGCAACCTAGAAACAAAAAGTT
19445306 TCTCGCTGCAG
1 TCTCGCTGCAG
19445317 TGAGAATGTA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (39 bp):
TCTCGCTGCAGCGAAATTGCAACCTAGAAACAAAAAGTT
Found at i:19445630 original size:2 final size:2
Alignment explanation
Indices: 19445618--19445667 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
19445608 ACATATTTAC
*
19445618 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19445660 AT AT AT AT
1 AT AT AT AT
19445668 NNNNNNNNNN
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19449945 original size:21 final size:21
Alignment explanation
Indices: 19449921--19449969 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
19449911 TCAACGGAAC
*
19449921 GAGGGTTCCACTCAACTGCAT
1 GAGGGTTCCACTCAACTACAT
19449942 GAGGGTTCCACTCAACTACAT
1 GAGGGTTCCACTCAACTACAT
19449963 GAGGGTT
1 GAGGGTT
19449970 TCGTGTTAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (21 bp):
GAGGGTTCCACTCAACTACAT
Found at i:19450455 original size:38 final size:38
Alignment explanation
Indices: 19450354--19450455 Score: 95
Period size: 36 Copynumber: 2.7 Consensus size: 38
19450344 CTCACCTAGC
19450354 TCATGTGCATCCCCCCACATCGTGCACAAGCACAGACA
1 TCATGTGCATCCCCCCACATCGTGCACAAGCACAGACA
* * ** * * *
19450392 TCGTGTGC-T-CTCCCACATCACGCACATTTG-A-TGCCA
1 TCATGTGCATCCCCCCACATCGTGCACA--AGCACAGACA
19450428 TCATGTGCATCCCCCCACATCGTGCACA
1 TCATGTGCATCCCCCCACATCGTGCACA
19450456 CGGGCAATAT
Statistics
Matches: 49, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
36 24 0.49
37 3 0.06
38 22 0.45
ACGTcount: A:0.24, C:0.39, G:0.16, T:0.22
Consensus pattern (38 bp):
TCATGTGCATCCCCCCACATCGTGCACAAGCACAGACA
Found at i:19451129 original size:20 final size:20
Alignment explanation
Indices: 19451083--19451130 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
19451073 ATGGGAGGAA
19451083 GAAGAAT-AAGAAGCTGCTG
1 GAAGAATGAAGAAGCTGCTG
19451102 G-AGAAATGAAGAAGCTGCTG
1 GAAG-AATGAAGAAGCTGCTG
19451122 GAAGAATGA
1 GAAGAATGA
19451131 GATCTTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 2 0.08
19 4 0.15
20 18 0.69
21 2 0.08
ACGTcount: A:0.44, C:0.08, G:0.33, T:0.15
Consensus pattern (20 bp):
GAAGAATGAAGAAGCTGCTG
Found at i:19452321 original size:2 final size:2
Alignment explanation
Indices: 19452303--19452341 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
19452293 ACATAGATAT
* *
19452303 AC AC GC AC AC GC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
19452342 TATATATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.49, G:0.05, T:0.00
Consensus pattern (2 bp):
AC
Found at i:19454456 original size:43 final size:43
Alignment explanation
Indices: 19454337--19454458 Score: 120
Period size: 43 Copynumber: 2.8 Consensus size: 43
19454327 TGACTCAGCT
* * ****
19454337 ATGTGTGAGTAGGGAGTGCGCACAAGCTGAG-GATGACCCGGTT
1 ATGTGCGAGTAGGGAGTGCGCATAAGCTG-GTGATGACCCAACC
* * * **
19454380 ATATGCGAGTGGGGAGTGCGCATAACCCAGTGATGACCCAACC
1 ATGTGCGAGTAGGGAGTGCGCATAAGCTGGTGATGACCCAACC
*
19454423 ATGTGCGAGTAGGGAGTGCGCATGAGCTGGTGATGA
1 ATGTGCGAGTAGGGAGTGCGCATAAGCTGGTGATGA
19454459 TGATGATGAT
Statistics
Matches: 61, Mismatches: 17, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
42 1 0.02
43 60 0.98
ACGTcount: A:0.25, C:0.18, G:0.38, T:0.20
Consensus pattern (43 bp):
ATGTGCGAGTAGGGAGTGCGCATAAGCTGGTGATGACCCAACC
Found at i:19454482 original size:22 final size:23
Alignment explanation
Indices: 19454450--19454493 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
19454440 GCGCATGAGC
19454450 TGGTGATGATGATGATGATGGGA
1 TGGTGATGATGATGATGATGGGA
19454473 TGGTG-TGATGATGATGATGGG
1 TGGTGATGATGATGATGATGGG
19454494 TATATGCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.23, C:0.00, G:0.45, T:0.32
Consensus pattern (23 bp):
TGGTGATGATGATGATGATGGGA
Found at i:19463306 original size:36 final size:36
Alignment explanation
Indices: 19463250--19463340 Score: 119
Period size: 36 Copynumber: 2.5 Consensus size: 36
19463240 ATAGGGTTAG
* *
19463250 GTGTAACCTTTACAACATGCCTTTTAACAAGATCAA
1 GTGTAACCTTCAAAACATGCCTTTTAACAAGATCAA
* * *
19463286 GTGTAACCTTCAAAATATGCCTTTTCACAAGATCAG
1 GTGTAACCTTCAAAACATGCCTTTTAACAAGATCAA
19463322 GTGTAACCTTACCAAAACA
1 GTGTAACCTT--CAAAACA
19463341 CTATCTTTTC
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
36 41 0.87
38 6 0.13
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.29
Consensus pattern (36 bp):
GTGTAACCTTCAAAACATGCCTTTTAACAAGATCAA
Found at i:19468052 original size:26 final size:25
Alignment explanation
Indices: 19468023--19468080 Score: 62
Period size: 26 Copynumber: 2.3 Consensus size: 25
19468013 ATTTTCTAGT
* * *
19468023 TTTCCTTTGTTTTTCTCTTTTCTTCC
1 TTTCCTTTCTATTTCTCTCTTCTT-C
* *
19468049 TTTCCTCTCTATTTCTCTCTTGTTC
1 TTTCCTTTCTATTTCTCTCTTCTTC
19468074 TTTCCTT
1 TTTCCTT
19468081 ATGGCCAGCC
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
25 7 0.27
26 19 0.73
ACGTcount: A:0.02, C:0.29, G:0.03, T:0.66
Consensus pattern (25 bp):
TTTCCTTTCTATTTCTCTCTTCTTC
Found at i:19474895 original size:29 final size:28
Alignment explanation
Indices: 19474844--19475017 Score: 195
Period size: 28 Copynumber: 6.0 Consensus size: 28
19474834 ATGACACTTT
*
19474844 AACATGTTTGTTTTAATTTAGACAAGAA
1 AACATGTTTGTCTTAATTTAGACAAGAA
19474872 AACATGTTTGGTCTTAATTTAGACAAGAA
1 AACATGTTT-GTCTTAATTTAGACAAGAA
*
19474901 AATATGTTTGTCTTAATTTAGGACAAGAAA
1 AACATGTTTGTCTTAATTTA-GACAAG-AA
* * *
19474931 AATATTTTTTGTCTTAATCTAGACAAGAA
1 AACA-TGTTTGTCTTAATTTAGACAAGAA
* *
19474960 AACATATTTGTCTCAATTTAGACAAGATAA
1 AACATGTTTGTCTTAATTTAGACAAG--AA
* * *
19474990 AATATTTTTGTCTTAATTAAAGACAAGA
1 AACATGTTTGTCTTAATT-TAGACAAGA
19475018 GTTTTCTTAA
Statistics
Matches: 127, Mismatches: 12, Indels: 13
0.84 0.08 0.09
Matches are distributed among these distances:
28 39 0.31
29 38 0.30
30 29 0.23
31 21 0.17
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.37
Consensus pattern (28 bp):
AACATGTTTGTCTTAATTTAGACAAGAA
Found at i:19474958 original size:59 final size:58
Alignment explanation
Indices: 19474844--19475006 Score: 222
Period size: 59 Copynumber: 2.8 Consensus size: 58
19474834 ATGACACTTT
* * * * *
19474844 AACATGTTTGTTTTAATTTAGACAAG-AAAACATGTTTGGTCTTAATTTAGACAAGAA
1 AACATGTTTGTCTTAATTTAGACAAGAAAAATATTTTTTGTCTTAATCTAGACAAGAA
*
19474901 AATATGTTTGTCTTAATTTAGGACAAGAAAAATATTTTTTGTCTTAATCTAGACAAGAA
1 AACATGTTTGTCTTAATTTA-GACAAGAAAAATATTTTTTGTCTTAATCTAGACAAGAA
* *
19474960 AACATATTTGTCTCAATTTAGACAAGATAAAATA-TTTTTGTCTTAAT
1 AACATGTTTGTCTTAATTTAGACAAGA-AAAATATTTTTTGTCTTAAT
19475007 TAAAGACAAG
Statistics
Matches: 94, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
57 18 0.19
58 26 0.28
59 50 0.53
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (58 bp):
AACATGTTTGTCTTAATTTAGACAAGAAAAATATTTTTTGTCTTAATCTAGACAAGAA
Found at i:19475181 original size:17 final size:17
Alignment explanation
Indices: 19475159--19475191 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
19475149 ATAATAATAA
19475159 AATAA-GAGTTATTATTC
1 AATAAGGAGTT-TTATTC
19475176 AATAAGGAGTTTTATT
1 AATAAGGAGTTTTATT
19475192 TTATCAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (17 bp):
AATAAGGAGTTTTATTC
Found at i:19476542 original size:30 final size:30
Alignment explanation
Indices: 19476508--19476593 Score: 71
Period size: 30 Copynumber: 3.1 Consensus size: 30
19476498 TCCCACCTCG
19476508 CACATGGCATATATCATCAGTGTGTGCACT
1 CACATGGCATATATCATCAGTGTGTGCACT
* * * * *
19476538 CACATAGC----A-CACCA--CTAT-CACG
1 CACATGGCATATATCATCAGTGTGTGCACT
19476560 CACATGGCATATATCATCAGTGTGTGCACT
1 CACATGGCATATATCATCAGTGTGTGCACT
19476590 CACA
1 CACA
19476594 CAGCACACCA
Statistics
Matches: 38, Mismatches: 10, Indels: 16
0.59 0.16 0.25
Matches are distributed among these distances:
22 10 0.26
23 2 0.05
25 4 0.11
26 2 0.05
27 4 0.11
29 2 0.05
30 14 0.37
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.24
Consensus pattern (30 bp):
CACATGGCATATATCATCAGTGTGTGCACT
Found at i:19476584 original size:52 final size:52
Alignment explanation
Indices: 19476506--19476662 Score: 269
Period size: 52 Copynumber: 3.0 Consensus size: 52
19476496 AGTCCCACCT
*
19476506 CGCACATGGCATATATCATCAGTGTGTGCACTCACATAGCACACCACTATCA
1 CGCACATGGCATATATCATCAGTGTGTGCACTCACAAAGCACACCACTATCA
*
19476558 CGCACATGGCATATATCATCAGTGTGTGCACTCACACAGCACACCACTATCA
1 CGCACATGGCATATATCATCAGTGTGTGCACTCACAAAGCACACCACTATCA
* * *
19476610 TGCACATGGCATATATCATCAATGTGTGCACTCATAAAGCACACCACTATCA
1 CGCACATGGCATATATCATCAGTGTGTGCACTCACAAAGCACACCACTATCA
19476662 C
1 C
19476663 CATCATGTGC
Statistics
Matches: 99, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 99 1.00
ACGTcount: A:0.32, C:0.31, G:0.15, T:0.23
Consensus pattern (52 bp):
CGCACATGGCATATATCATCAGTGTGTGCACTCACAAAGCACACCACTATCA
Found at i:19486886 original size:107 final size:107
Alignment explanation
Indices: 19486700--19486913 Score: 403
Period size: 107 Copynumber: 2.0 Consensus size: 107
19486690 TCACTGTTTC
19486700 AGGAGTCGAATTCCAAGTACTCCGATTCTTGATCCTCGGGGTACTATCTCTTTACTTTTGCCAGA
1 AGGAGTCGAATTCCAAGTACTCCGATTCTTGATCCTCGGGGTACTATCTCTTTACTTTTGCCAGA
*
19486765 ATGCTCCCCACCTAGACATAATGC-CAATAAGCCATTTACTA
66 ATGCTCACCACCTAGACATAATGCACAATAAGCCATTTACTA
19486806 NAGGAGTCGAATTCCAAGTACTCCGATTCTTGATCCTCGGGGTACTATCTCTTTACTTTTGCCAG
1 -AGGAGTCGAATTCCAAGTACTCCGATTCTTGATCCTCGGGGTACTATCTCTTTACTTTTGCCAG
19486871 AATGCTCACCACCTAGACATAATGCACAATAAGCCATTTACTA
65 AATGCTCACCACCTAGACATAATGCACAATAAGCCATTTACTA
19486914 TATTGTGCTA
Statistics
Matches: 105, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
107 88 0.84
108 17 0.16
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (107 bp):
AGGAGTCGAATTCCAAGTACTCCGATTCTTGATCCTCGGGGTACTATCTCTTTACTTTTGCCAGA
ATGCTCACCACCTAGACATAATGCACAATAAGCCATTTACTA
Found at i:19489858 original size:2 final size:2
Alignment explanation
Indices: 19489851--19489875 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19489841 TATAATGTTG
19489851 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 A
19489876 CTATGTCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19490091 original size:54 final size:54
Alignment explanation
Indices: 19490033--19490178 Score: 193
Period size: 54 Copynumber: 2.7 Consensus size: 54
19490023 ACTGTGCATG
* * * * *
19490033 ATGTGAGGGGATGAAAACGAGTTGGGTGAGATGGGGTGTCCGGCTATGTGCACA
1 ATGTGGGGGGATGCACATGAGTTGGGTGAGATGGGGTGTCCAGCTATGTGCACA
* * **
19490087 ATGTGGGGGGATGCACATGAGCTAGGTGAGATGGGGTGTCCAGCTATGTGCATG
1 ATGTGGGGGGATGCACATGAGTTGGGTGAGATGGGGTGTCCAGCTATGTGCACA
* *
19490141 ATGTGGGGGGATGCACATGAGTTGGATGAGATGTGGTG
1 ATGTGGGGGGATGCACATGAGTTGGGTGAGATGGGGTG
19490179 GTATACTAAT
Statistics
Matches: 79, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 79 1.00
ACGTcount: A:0.22, C:0.10, G:0.44, T:0.24
Consensus pattern (54 bp):
ATGTGGGGGGATGCACATGAGTTGGGTGAGATGGGGTGTCCAGCTATGTGCACA
Found at i:19493125 original size:2 final size:2
Alignment explanation
Indices: 19493118--19493144 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19493108 ATTATGTTGG
19493118 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
19493145 GTTGTGCCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19493216 original size:2 final size:2
Alignment explanation
Indices: 19493209--19493235 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19493199 CTATATGTTG
19493209 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
19493236 GTTGTGCCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19493256 original size:91 final size:91
Alignment explanation
Indices: 19493095--19493281 Score: 333
Period size: 91 Copynumber: 2.1 Consensus size: 91
19493085 GTTATGGATT
*
19493095 TGTGCACTACTACATTATGTTGGTATATATATATATATATATATATATATGTTGTGCCTTGGTAG
1 TGTGTACTACTACATTATGTTGGTATATATATATATATATATATATATATGTTGTGCCTTGGTAG
19493160 TTGATATTGTGTGATAATTATAACCG
66 TTGATATTGTGTGATAATTATAACCG
19493186 TGTGTNACTACTAC-TATATGTT-GTATATATATATATATATATATATATATGTTGTGCCTTGGT
1 TGTGT-ACTACTACAT-TATGTTGGTATATATATATATATATATATATATATGTTGTGCCTTGGT
19493249 AGTTGATATTGTGTGATAATTATAACCG
64 AGTTGATATTGTGTGATAATTATAACCG
19493277 TGTGT
1 TGTGT
19493282 GGGCACGATG
Statistics
Matches: 93, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
91 79 0.85
92 14 0.15
ACGTcount: A:0.29, C:0.08, G:0.18, T:0.45
Consensus pattern (91 bp):
TGTGTACTACTACATTATGTTGGTATATATATATATATATATATATATATGTTGTGCCTTGGTAG
TTGATATTGTGTGATAATTATAACCG
Found at i:19493409 original size:38 final size:39
Alignment explanation
Indices: 19493353--19493458 Score: 108
Period size: 38 Copynumber: 2.7 Consensus size: 39
19493343 ACAGTGCCCG
* * * *
19493353 TGTGCACGATAT-AGGGGGATGTACATGATGGCACTAAC-
1 TGTGCACGATGTGA-GGGGATGCACATGATGACACCAACA
* * *
19493391 TGTGCACGATGTGAGGGGATGCACACGATGACTCCGACTA
1 TGTGCACGATGTGAGGGGATGCACATGATGACACCAAC-A
*
19493431 TGTGCACGATGTGGGGGGATGCACATGA
1 TGTGCACGATGTGAGGGGATGCACATGA
19493459 GCTAGGTGAA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
38 29 0.52
39 1 0.02
40 26 0.46
ACGTcount: A:0.25, C:0.18, G:0.35, T:0.22
Consensus pattern (39 bp):
TGTGCACGATGTGAGGGGATGCACATGATGACACCAACA
Found at i:19496526 original size:35 final size:35
Alignment explanation
Indices: 19496479--19496619 Score: 194
Period size: 35 Copynumber: 4.0 Consensus size: 35
19496469 GGAATGCGTG
*
19496479 TGATGATATTGAAGTGTTCGAGTAGGGAGTGCACA
1 TGATGATATTGAAGTGTGCGAGTAGGGAGTGCACA
*
19496514 CGATGATATTGAAGTGTGCGAGTAGGGAGTGCACA
1 TGATGATATTGAAGTGTGCGAGTAGGGAGTGCACA
* *
19496549 TGATGATATAGAAATGTGCGAGTAGGGAGTGCACA
1 TGATGATATTGAAGTGTGCGAGTAGGGAGTGCACA
* ***
19496584 TAATGATATTGCCTTGTGC-ATGTAGGGAGTGCACA
1 TGATGATATTGAAGTGTGCGA-GTAGGGAGTGCACA
19496619 T
1 T
19496620 TGGCTAAGTG
Statistics
Matches: 95, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
34 1 0.01
35 94 0.99
ACGTcount: A:0.29, C:0.11, G:0.33, T:0.27
Consensus pattern (35 bp):
TGATGATATTGAAGTGTGCGAGTAGGGAGTGCACA
Found at i:19509193 original size:36 final size:36
Alignment explanation
Indices: 19509116--19509194 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 36
19509106 TAACCATGCA
* * *
19509116 TGTGTGGTGTGGGAGTGCACATGACGGTGCCGGTGG
1 TGTGTGGTGTGGGAGTGCAAATGACGGTGACGATGG
* *
19509152 TGTGTGGTGTGGGAGTGCAAATGCCGGTGATGAT-G
1 TGTGTGGTGTGGGAGTGCAAATGACGGTGACGATGG
19509187 TGGTGTGG
1 T-GTGTGG
19509195 GAGTGTATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 2 0.05
36 35 0.95
ACGTcount: A:0.13, C:0.10, G:0.49, T:0.28
Consensus pattern (36 bp):
TGTGTGGTGTGGGAGTGCAAATGACGGTGACGATGG
Found at i:19516344 original size:35 final size:36
Alignment explanation
Indices: 19516256--19516344 Score: 103
Period size: 36 Copynumber: 2.5 Consensus size: 36
19516246 CTCATCAGCT
* *
19516256 CATGTGCACTCCGACACCGCACATAGCTAGAATCAT
1 CATGTGCACTCCAACACCGCACATAGCTAGAATCAC
*
19516292 CATGTGCACTCCCACACCGCACA-AGGC-A-ACATCAC
1 CATGTGCACTCCAACACCGCACATA-GCTAGA-ATCAC
*
19516327 CATGTGCACTTCAACACC
1 CATGTGCACTCCAACACC
19516345 ACATCATCAC
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
34 1 0.02
35 22 0.47
36 24 0.51
ACGTcount: A:0.30, C:0.38, G:0.15, T:0.17
Consensus pattern (36 bp):
CATGTGCACTCCAACACCGCACATAGCTAGAATCAC
Found at i:19516952 original size:43 final size:43
Alignment explanation
Indices: 19516906--19517042 Score: 204
Period size: 43 Copynumber: 3.2 Consensus size: 43
19516896 GTTATGTGAT
* *
19516906 GATGATGACCCAGCTATGTGCGATGT-GAGAGTGCACATAAGCT
1 GATGATGACCCAGCTATGTGCGA-GTAGGGAGTGCACATAAGCC
*
19516949 GATGATGACCCAACTATGTGCGAGTAGGGAGTGCACATAAGCC
1 GATGATGACCCAGCTATGTGCGAGTAGGGAGTGCACATAAGCC
* * *
19516992 GATGATGACCTAGCTATGTACGAGTAGGGAGTGCGCATAAGCC
1 GATGATGACCCAGCTATGTGCGAGTAGGGAGTGCACATAAGCC
19517035 GATGATGA
1 GATGATGA
19517043 TGACTCGACT
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
42 2 0.02
43 84 0.98
ACGTcount: A:0.29, C:0.18, G:0.31, T:0.21
Consensus pattern (43 bp):
GATGATGACCCAGCTATGTGCGAGTAGGGAGTGCACATAAGCC
Found at i:19522733 original size:43 final size:43
Alignment explanation
Indices: 19522663--19522781 Score: 177
Period size: 43 Copynumber: 2.8 Consensus size: 43
19522653 GTAATTATGT
* *
19522663 TGACTCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGAG-GA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCG-GTGA
*
19522706 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
* *
19522749 TGACCCAGCCATGTGCGAGTAGGGAGTGCGCAT
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCAT
19522782 GAGCTGGTGA
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
42 1 0.01
43 68 0.99
ACGTcount: A:0.22, C:0.21, G:0.38, T:0.19
Consensus pattern (43 bp):
TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
Found at i:19522791 original size:43 final size:43
Alignment explanation
Indices: 19522673--19522794 Score: 174
Period size: 43 Copynumber: 2.8 Consensus size: 43
19522663 TGACTCGGCT
* **
19522673 ATGTGCGAGTAGGGAGTGCGCATAAGCCGAG-GATGACCCGGTT
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCG-GTGATGACCCAGCC
*
19522716 ATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCAGCC
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCC
* *
19522759 ATGTGCGAGTAGGGAGTGCGCATGAGCTGGTGATGA
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGA
19522795 TGATGATGAG
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
42 1 0.01
43 70 0.99
ACGTcount: A:0.23, C:0.19, G:0.39, T:0.19
Consensus pattern (43 bp):
ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCC
Found at i:19522805 original size:20 final size:20
Alignment explanation
Indices: 19522780--19522842 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
19522770 GGGAGTGCGC
19522780 ATGAGCTGGTGATGATGATG
1 ATGAGCTGGTGATGATGATG
19522800 ATGAGCTGGTGATGATGATG
1 ATGAGCTGGTGATGATGATG
* *
19522820 ATGGGTTGGTGA-GATGATG
1 ATGAGCTGGTGATGATGATG
19522839 ATGA
1 ATGA
19522843 TGGGTATATA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 10 0.25
20 30 0.75
ACGTcount: A:0.25, C:0.03, G:0.41, T:0.30
Consensus pattern (20 bp):
ATGAGCTGGTGATGATGATG
Found at i:19531943 original size:42 final size:42
Alignment explanation
Indices: 19531896--19532104 Score: 328
Period size: 42 Copynumber: 5.0 Consensus size: 42
19531886 CATCTCATAT
* *
19531896 GCAACGGCTTATGTGTACTCCCACTCGCATATAGCCGGGTCA
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
* ** *
19531938 GCAACGACTTATGTGCACTCTTACTCGCACATAGCCGAGTCA
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
*
19531980 GCAACGGCTTATGTGCACTCCCACTAGCACATAGCCGGGTCA
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
*
19532022 GCAACGGCTTATGTGCACTCCCACTCGCACATAGTCGGGTCA
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
* *
19532064 ACAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTC
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTC
19532105 CACATTAACA
Statistics
Matches: 151, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 151 1.00
ACGTcount: A:0.23, C:0.33, G:0.22, T:0.22
Consensus pattern (42 bp):
GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
Found at i:19540300 original size:37 final size:37
Alignment explanation
Indices: 19540248--19540393 Score: 231
Period size: 37 Copynumber: 3.9 Consensus size: 37
19540238 TTCATCGTCA
* *
19540248 TGTGCACTCCATACTCGCACA-TTCTATCATCATCATG
1 TGTGCACTCCCTACTCGCACACTTC-AACATCATCATG
19540285 TGTGCACTCCCTACTCGCACACTTCAACATCATCATG
1 TGTGCACTCCCTACTCGCACACTTCAACATCATCATG
*
19540322 TGTGCACTCTCTACTCGCACACTTCAACATCATCATG
1 TGTGCACTCCCTACTCGCACACTTCAACATCATCATG
**
19540359 TGTGCACTCCCTACTCAAACACTTCAACATCATCA
1 TGTGCACTCCCTACTCGCACACTTCAACATCATCA
19540394 CACAACATTA
Statistics
Matches: 102, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
37 99 0.97
38 3 0.03
ACGTcount: A:0.26, C:0.36, G:0.10, T:0.29
Consensus pattern (37 bp):
TGTGCACTCCCTACTCGCACACTTCAACATCATCATG
Found at i:19541091 original size:20 final size:20
Alignment explanation
Indices: 19541068--19541107 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
19541058 AGAAAAACAA
19541068 GAAGCTACTAGAAAAATGAG
1 GAAGCTACTAGAAAAATGAG
* * *
19541088 GAAGCTGCTGGAGAAATGAG
1 GAAGCTACTAGAAAAATGAG
19541108 ATATTTATAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.10, G:0.33, T:0.15
Consensus pattern (20 bp):
GAAGCTACTAGAAAAATGAG
Found at i:19548091 original size:19 final size:19
Alignment explanation
Indices: 19548064--19548114 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
19548054 GATGGGAGGA
* *
19548064 AGAAGAATGAGAAGCTGTT
1 AGAAAAATGAGAAGCTGCT
*
19548083 AGAAAAATGAAGAAGTTGCT
1 AGAAAAATG-AGAAGCTGCT
*
19548103 AGAGAAATGAGA
1 AGAAAAATGAGA
19548115 TATTAATAGC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.49, C:0.04, G:0.29, T:0.18
Consensus pattern (19 bp):
AGAAAAATGAGAAGCTGCT
Found at i:19550191 original size:29 final size:28
Alignment explanation
Indices: 19550050--19550220 Score: 144
Period size: 29 Copynumber: 5.9 Consensus size: 28
19550040 TTAAGATAAC
* *
19550050 TCTTGTCTTTAATTAAGACAAAAATATTTT
1 TCTTGTC-TAAATTAAGACAAACATA-TTT
* * **
19550080 ATCTTGTCTAAATTGAGACAAATATGCTT
1 -TCTTGTCTAAATTAAGACAAACATATTT
* * *
19550109 TCTTGTCTAGATTAAGATAAAAAATAATTT
1 TCTTGTCTAAATTAAGA-CAAACAT-ATTT
* * *
19550139 TCTTATTTTAAATTAAGACGAACATATTT
1 TCTT-GTCTAAATTAAGACAAACATATTT
*
19550168 TCTTGTCTAAATTAAGATCAAACATGTTT
1 TCTTGTCTAAATTAAGA-CAAACATATTT
* *
19550197 TGTTGTCTAAATTAAAACAAACAT
1 TCTTGTCTAAATTAAGACAAACAT
19550221 GTTAAAGCTA
Statistics
Matches: 113, Mismatches: 23, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
28 33 0.29
29 39 0.35
30 24 0.21
31 17 0.15
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (28 bp):
TCTTGTCTAAATTAAGACAAACATATTT
Found at i:19552137 original size:20 final size:20
Alignment explanation
Indices: 19552082--19552138 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
19552072 TTTTGCCTGA
* *
19552082 AATGTATCGATACATGCCCC
1 AATGTATTGATACATTCCCC
19552102 AATGTATTGATACATTCCCC
1 AATGTATTGATACATTCCCC
19552122 AATGTATTGATACATTC
1 AATGTATTGATACATTC
19552139 ATTCAAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.33
Consensus pattern (20 bp):
AATGTATTGATACATTCCCC
Found at i:19555022 original size:38 final size:38
Alignment explanation
Indices: 19554940--19555038 Score: 101
Period size: 38 Copynumber: 2.6 Consensus size: 38
19554930 AGCTCATGTG
* *
19554940 CATCCCCCCACATCGTGCACATAGCCGAAGTCATCGCGTG
1 CATCCCCCCACATCGTGCAC--AGCCGAAGCCATCGCGTA
** *
19554980 CATCCCCCCACATCGTGCACAG-TTAATGCCATCGTGTA
1 CATCCCCCCACATCGTGCACAGCCGAA-GCCATCGCGTA
* *
19555018 CATCCCCCAACATTGTGCACA
1 CATCCCCCCACATCGTGCACA
19555039 TGGGCAATAT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
37 2 0.04
38 29 0.57
40 20 0.39
ACGTcount: A:0.24, C:0.39, G:0.16, T:0.20
Consensus pattern (38 bp):
CATCCCCCCACATCGTGCACAGCCGAAGCCATCGCGTA
Found at i:19555783 original size:20 final size:20
Alignment explanation
Indices: 19555758--19555803 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
19555748 CATGGAAGAT
*
19555758 GAAGAAACGCGATATGGGAG
1 GAAGAAACACGATATGGGAG
*
19555778 GAAGAAACACGATATGGGGG
1 GAAGAAACACGATATGGGAG
19555798 GAAGAA
1 GAAGAA
19555804 GAACAAGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.43, C:0.09, G:0.39, T:0.09
Consensus pattern (20 bp):
GAAGAAACACGATATGGGAG
Found at i:19557031 original size:28 final size:29
Alignment explanation
Indices: 19556990--19557049 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
19556980 GTCTATGGGC
* *
19556990 AATTTTTCAGTTTT-TGGGGCAAAAATGT
1 AATTTTTCACTTTTAGGGGGCAAAAATGT
* *
19557018 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCACTTTTA-GGGGGCAAAAATGT
19557048 AA
1 AA
19557050 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.30, C:0.08, G:0.23, T:0.38
Consensus pattern (29 bp):
AATTTTTCACTTTTAGGGGGCAAAAATGT
Found at i:19569390 original size:20 final size:20
Alignment explanation
Indices: 19569367--19569409 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
19569357 ACTTTAAAAT
19569367 AGAAACAACTTAATCGACTA
1 AGAAACAACTTAATCGACTA
** * *
19569387 AGAAGGAAGTTAGTCGACTA
1 AGAAACAACTTAATCGACTA
19569407 AGA
1 AGA
19569410 GCTCACTACC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.47, C:0.14, G:0.21, T:0.19
Consensus pattern (20 bp):
AGAAACAACTTAATCGACTA
Found at i:19572728 original size:19 final size:19
Alignment explanation
Indices: 19572704--19572743 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
19572694 ACAAGTGAAA
19572704 ATTTTATTAATAAAATAAT
1 ATTTTATTAATAAAATAAT
*
19572723 ATTTTATTAATAAACTAAT
1 ATTTTATTAATAAAATAAT
19572742 AT
1 AT
19572744 GAAAATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTTTATTAATAAAATAAT
Found at i:19574273 original size:54 final size:54
Alignment explanation
Indices: 19574119--19574273 Score: 238
Period size: 54 Copynumber: 2.9 Consensus size: 54
19574109 GATACCGTCT
* * * *
19574119 AGCTATGTGCACGATGTGGTGGGATGCACATAAGCTGGGTGAGATGAGATGTTT
1 AGCTATGTGCACGATGTGGTGGGATGCACATGAGTTGGGTGAGATGGGATGTTC
* * *
19574173 GGCTATATGCACGATGTGGTGGGATGCACATGCGTTGGGTGAGATGGGATGTTC
1 AGCTATGTGCACGATGTGGTGGGATGCACATGAGTTGGGTGAGATGGGATGTTC
*
19574227 AGCTATGTGCACAATGTGGTGGGATGCACATGAGTTGGGTGAGATGG
1 AGCTATGTGCACGATGTGGTGGGATGCACATGAGTTGGGTGAGATGG
19574274 AATGATTGCT
Statistics
Matches: 90, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 90 1.00
ACGTcount: A:0.22, C:0.12, G:0.39, T:0.27
Consensus pattern (54 bp):
AGCTATGTGCACGATGTGGTGGGATGCACATGAGTTGGGTGAGATGGGATGTTC
Found at i:19578286 original size:37 final size:37
Alignment explanation
Indices: 19578229--19578347 Score: 159
Period size: 37 Copynumber: 3.2 Consensus size: 37
19578219 CATATACATA
* * *
19578229 CATCGTCATCATGTGCGCACTCTCTACTCACACACTC
1 CATCATCATCATGTGTGCACTCTCTACTCGCACACTC
*
19578266 TATCATCATCATGTGTGCACT-TCATACTCGCACACTC
1 CATCATCATCATGTGTGCACTCTC-TACTCGCACACTC
* *
19578303 CATCATCATCATGTGTGCACTCCCTACTCGCACACTT
1 CATCATCATCATGTGTGCACTCTCTACTCGCACACTC
*
19578340 CAACATCA
1 CATCATCA
19578348 CCACCCAACA
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
36 2 0.03
37 69 0.96
38 1 0.01
ACGTcount: A:0.24, C:0.37, G:0.10, T:0.29
Consensus pattern (37 bp):
CATCATCATCATGTGTGCACTCTCTACTCGCACACTC
Found at i:19585093 original size:40 final size:40
Alignment explanation
Indices: 19585049--19585170 Score: 117
Period size: 40 Copynumber: 3.1 Consensus size: 40
19585039 AGGGAGATGG
*
19585049 ATGATAATAGTGCTAATGTGCACGATGTGGGGGGATGTAC
1 ATGATAATAGTGCTAATGTGCACGATGTGGGGGGATGCAC
*** * *
19585089 ATGATGGCACTG--ATTGTGCACGATGTGGGGGGATGCAC
1 ATGATAATAGTGCTAATGTGCACGATGTGGGGGGATGCAC
* * *
19585127 ATGATGACTCCG-GCT-ATGTGCACGATGTGGGGGGATACAC
1 ATGAT-AAT-AGTGCTAATGTGCACGATGTGGGGGGATGCAC
19585167 ATGA
1 ATGA
19585171 GCTGGAAGTG
Statistics
Matches: 65, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
38 29 0.45
39 1 0.02
40 35 0.54
ACGTcount: A:0.25, C:0.15, G:0.36, T:0.25
Consensus pattern (40 bp):
ATGATAATAGTGCTAATGTGCACGATGTGGGGGGATGCAC
Found at i:19585107 original size:38 final size:40
Alignment explanation
Indices: 19585064--19585170 Score: 146
Period size: 38 Copynumber: 2.7 Consensus size: 40
19585054 AATAGTGCTA
* * *
19585064 ATGTGCACGATGTGGGGGGATGTACATGATGGC-ACTGAT
1 ATGTGCACGATGTGGGGGGATGCACATGATGACTACGGAT
* *
19585103 -TGTGCACGATGTGGGGGGATGCACATGATGACTCCGGCT
1 ATGTGCACGATGTGGGGGGATGCACATGATGACTACGGAT
*
19585142 ATGTGCACGATGTGGGGGGATACACATGA
1 ATGTGCACGATGTGGGGGGATGCACATGA
19585171 GCTGGAAGTG
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
38 30 0.50
39 3 0.05
40 27 0.45
ACGTcount: A:0.22, C:0.16, G:0.38, T:0.23
Consensus pattern (40 bp):
ATGTGCACGATGTGGGGGGATGCACATGATGACTACGGAT
Found at i:19591895 original size:54 final size:54
Alignment explanation
Indices: 19591831--19592044 Score: 270
Period size: 54 Copynumber: 4.0 Consensus size: 54
19591821 GATGGTGATA
* *
19591831 ATGTTCGGCTATGTGCACGATGTGGGAGGATGCACATGAGCTGGGTCAGATGGG
1 ATGTCCGGCTATGTGCACGATGTGGGAGGATGCACATGAGCTGGGTGAGATGGG
** * * *
19591885 ATGTTTGGCTATGTGCACGATGTAAGGA-GATGAACATGAGTTGGGTGAGATGGG
1 ATGTCCGGCTATGTGCACGATGT-GGGAGGATGCACATGAGCTGGGTGAGATGGG
* *
19591939 ATGTCCAGCTATGTGCACGATGTGAGG-GGATGCACATGAGCTGGGTGTGATGGG
1 ATGTCCGGCTATGTGCACGATGTG-GGAGGATGCACATGAGCTGGGTGAGATGGG
* * * * *
19591993 GTGTCTGGCTATGTGCACAATGTGGGGGGATGCACATGAGCTGGATGAGATG
1 ATGTCCGGCTATGTGCACGATGTGGGAGGATGCACATGAGCTGGGTGAGATG
19592045 TGGTGGTATA
Statistics
Matches: 138, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
53 2 0.01
54 133 0.96
55 3 0.02
ACGTcount: A:0.22, C:0.13, G:0.40, T:0.25
Consensus pattern (54 bp):
ATGTCCGGCTATGTGCACGATGTGGGAGGATGCACATGAGCTGGGTGAGATGGG
Found at i:19591970 original size:108 final size:108
Alignment explanation
Indices: 19591838--19592044 Score: 299
Period size: 108 Copynumber: 1.9 Consensus size: 108
19591828 ATAATGTTCG
*
19591838 GCTATGTGCACGATGTGGGAGGATGCACATGAGCTGGGTCAGATGGGATGTTTGGCTATGTGCAC
1 GCTATGTGCACGATGTGGGAGGATGCACATGAGCTGGGTCAGATGGGATGTCTGGCTATGTGCAC
* * *
19591903 GATGTAAGGAGATGAACATGAGTTGGGTGAGATGGGATGTCCA
66 AATGTAAGGAGATGAACATGAGCTGGATGAGATGGGATGTCCA
** *
19591946 GCTATGTGCACGATGTGAGG-GGATGCACATGAGCTGGGTGTGATGGGGTGTCTGGCTATGTGCA
1 GCTATGTGCACGATGTG-GGAGGATGCACATGAGCTGGGTCAGATGGGATGTCTGGCTATGTGCA
** * *
19592010 CAATGTGGGGGGATGCACATGAGCTGGATGAGATG
65 CAATGTAAGGAGATGAACATGAGCTGGATGAGATG
19592045 TGGTGGTATA
Statistics
Matches: 87, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
108 85 0.98
109 2 0.02
ACGTcount: A:0.22, C:0.13, G:0.41, T:0.25
Consensus pattern (108 bp):
GCTATGTGCACGATGTGGGAGGATGCACATGAGCTGGGTCAGATGGGATGTCTGGCTATGTGCAC
AATGTAAGGAGATGAACATGAGCTGGATGAGATGGGATGTCCA
Found at i:19601121 original size:16 final size:16
Alignment explanation
Indices: 19601100--19601132 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
19601090 TTAATTAATT
19601100 TCCTAAGGTTCTACCA
1 TCCTAAGGTTCTACCA
19601116 TCCTAAGGTTCTACCA
1 TCCTAAGGTTCTACCA
19601132 T
1 T
19601133 ACTTCTCCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.30, G:0.12, T:0.33
Consensus pattern (16 bp):
TCCTAAGGTTCTACCA
Found at i:19637144 original size:16 final size:15
Alignment explanation
Indices: 19637121--19637197 Score: 71
Period size: 13 Copynumber: 5.5 Consensus size: 15
19637111 GAGATCAATT
19637121 GGAAGAAAGGAGAAA
1 GGAAGAAAGGAGAAA
19637136 GGAA-AGAA--AGAAA
1 GGAAGA-AAGGAGAAA
19637149 GG-AGAAA-G-GAAA
1 GGAAGAAAGGAGAAA
*
19637161 GAAAGAAAGGAGAAA
1 GGAAGAAAGGAGAAA
19637176 -GAA-AAAGAGAGAAA
1 GGAAGAAAG-GAGAAA
19637190 GGAAGAAA
1 GGAAGAAA
19637198 AAGCTTGGTT
Statistics
Matches: 51, Mismatches: 2, Indels: 17
0.73 0.03 0.24
Matches are distributed among these distances:
12 8 0.16
13 17 0.33
14 10 0.20
15 13 0.25
16 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (15 bp):
GGAAGAAAGGAGAAA
Found at i:19637146 original size:4 final size:4
Alignment explanation
Indices: 19637131--19637197 Score: 52
Period size: 4 Copynumber: 17.2 Consensus size: 4
19637121 GGAAGAAAGG
* *
19637131 AGAA AGGAA AGAA AGAA AG-G AGAA AGGAA AGAA AGAA AG-G AGAA AG-A
1 AGAA A-GAA AGAA AGAA AGAA AGAA A-GAA AGAA AGAA AGAA AGAA AGAA
* *
19637178 A-AA AGAG AGAA AGGA AGAA A
1 AGAA AGAA AGAA AGAA AGAA A
19637198 AAGCTTGGTT
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
3 8 0.16
4 33 0.67
5 8 0.16
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:19637178 original size:24 final size:20
Alignment explanation
Indices: 19637123--19637197 Score: 114
Period size: 20 Copynumber: 3.6 Consensus size: 20
19637113 GATCAATTGG
19637123 AAGAAAGGAGAAAGGAAAGA
1 AAGAAAGGAGAAAGGAAAGA
19637143 AAGAAAGGAGAAAGGAAAGA
1 AAGAAAGGAGAAAGGAAAGA
*
19637163 AAGAAAGGAGAAAGAAAAAGA
1 AAGAAAGGAGAAAG-GAAAGA
*
19637184 GAGAAAGGAAGAAA
1 AAGAAAGG-AGAAA
19637198 AAGCTTGGTT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
20 34 0.67
21 12 0.24
22 5 0.10
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (20 bp):
AAGAAAGGAGAAAGGAAAGA
Done.