Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 58 of 175
Found at i:16995285 original size:13 final size:13
Alignment explanation
Indices: 16995267--16995308 Score: 75
Period size: 13 Copynumber: 3.2 Consensus size: 13
16995257 TAACTACTAT
16995267 TATTTTGTATCTA
1 TATTTTGTATCTA
*
16995280 TATTTTATATCTA
1 TATTTTGTATCTA
16995293 TATTTTGTATCTA
1 TATTTTGTATCTA
16995306 TAT
1 TAT
16995309 AACTATTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.26, C:0.07, G:0.05, T:0.62
Consensus pattern (13 bp):
TATTTTGTATCTA
Found at i:16996505 original size:42 final size:42
Alignment explanation
Indices: 16996459--16996564 Score: 115
Period size: 42 Copynumber: 2.5 Consensus size: 42
16996449 AATTGATATT
*
16996459 TGATTTGCATGTTAAACATGCCAACAATGAT-AAACTGAGATA
1 TGATTTGCATGTTAAGCATGCCAACAATGATGAAA-TGAGATA
* * * * * * * *
16996501 TGATTTGTATGTTAAGTATGCCGACTATGTTGATATTAGATT
1 TGATTTGCATGTTAAGCATGCCAACAATGATGAAATGAGATA
16996543 TGATTTGCATGTTAAGCATGCC
1 TGATTTGCATGTTAAGCATGCC
16996565 TACTGATAAT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
42 50 0.96
43 2 0.04
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.37
Consensus pattern (42 bp):
TGATTTGCATGTTAAGCATGCCAACAATGATGAAATGAGATA
Found at i:16997896 original size:23 final size:23
Alignment explanation
Indices: 16997824--16997899 Score: 116
Period size: 23 Copynumber: 3.3 Consensus size: 23
16997814 ATAAGTGCCA
16997824 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * *
16997847 CACCGATATGTAACCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
16997870 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
16997893 CACTGAT
1 CACTGAT
16997900 CAATAAGACT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:16999348 original size:24 final size:24
Alignment explanation
Indices: 16999271--16999361 Score: 89
Period size: 24 Copynumber: 3.8 Consensus size: 24
16999261 TACTACAAAA
16999271 ATTGAGTGGCTT-ATCCACAACGAT
1 ATTGAGTGGCTTGA-CCACAACGAT
* * *
16999295 A-TGAATGGCTTGTCCAGAAC-ACT
1 ATTGAGTGGCTTGACCACAACGA-T
**
16999318 AACGAGTGGCTTGACCACAACGAT
1 ATTGAGTGGCTTGACCACAACGAT
*
16999342 ATTGAGTGGCTTGGCCACAA
1 ATTGAGTGGCTTGACCACAA
16999362 TGTGGAGTGT
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
22 1 0.02
23 17 0.32
24 34 0.64
25 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (24 bp):
ATTGAGTGGCTTGACCACAACGAT
Found at i:16999463 original size:20 final size:21
Alignment explanation
Indices: 16999434--16999473 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
16999424 GGTAGGAAAA
16999434 TTTTGTAAAACTTGCACTGAT
1 TTTTGTAAAACTTGCACTGAT
*
16999455 TTTTG-AAAAGTTGCACTGA
1 TTTTGTAAAACTTGCACTGA
16999474 CATTCTCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.40
Consensus pattern (21 bp):
TTTTGTAAAACTTGCACTGAT
Found at i:17002101 original size:40 final size:40
Alignment explanation
Indices: 17002018--17002280 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
17002008 TTGAATGCTG
* * * * * *
17002018 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
17002058 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
17002098 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
17002138 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
17002178 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
17002218 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
17002257 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
17002281 TGAACGAGGA
Statistics
Matches: 201, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.17
40 158 0.79
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:17002300 original size:79 final size:80
Alignment explanation
Indices: 17002057--17002315 Score: 256
Period size: 80 Copynumber: 3.3 Consensus size: 80
17002047 AAGTGAATAT
* * * * * *
17002057 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** * *
17002121 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
17002137 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
** ** *
17002202 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * *
17002217 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
* *
17002281 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
17002296 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
17002316 TACGGATTTG
Statistics
Matches: 156, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
78 14 0.09
79 48 0.31
80 94 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
CGAACGAGGAGCTAA
Found at i:17009444 original size:40 final size:40
Alignment explanation
Indices: 17009361--17009623 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
17009351 TTGAATGCTG
* * * * * *
17009361 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
17009401 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
17009441 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
17009481 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
17009521 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
17009561 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
17009600 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
17009624 TGAACGAGGA
Statistics
Matches: 201, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.17
40 158 0.79
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:17009643 original size:79 final size:80
Alignment explanation
Indices: 17009400--17009658 Score: 256
Period size: 80 Copynumber: 3.3 Consensus size: 80
17009390 AAGTGAATAT
* * * * * *
17009400 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** * *
17009464 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
17009480 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
** ** *
17009545 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * *
17009560 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
* *
17009624 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
17009639 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
17009659 TACGGATTTG
Statistics
Matches: 156, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
78 14 0.09
79 48 0.31
80 94 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
CGAACGAGGAGCTAA
Found at i:17012466 original size:15 final size:15
Alignment explanation
Indices: 17012443--17012474 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
17012433 TTTAGATTGT
17012443 GATTGTGAAACTATA
1 GATTGTGAAACTATA
*
17012458 GATTTTGAAACTATA
1 GATTGTGAAACTATA
17012473 GA
1 GA
17012475 CTATGAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.06, G:0.19, T:0.34
Consensus pattern (15 bp):
GATTGTGAAACTATA
Found at i:17012481 original size:15 final size:15
Alignment explanation
Indices: 17012448--17012520 Score: 65
Period size: 15 Copynumber: 4.7 Consensus size: 15
17012438 ATTGTGATTG
* *
17012448 TGAAACTATAGATTT
1 TGAAACTATAGACTA
17012463 TGAAACTATAGACTA
1 TGAAACTATAGACTA
*
17012478 TGAAACAAATAGACTA
1 TGAAAC-TATAGACTA
* * * *
17012494 GGAAACTTTAGAGTC
1 TGAAACTATAGACTA
17012509 TGAAAACTATAG
1 TG-AAACTATAG
17012521 TGAAACTATG
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
15 25 0.54
16 21 0.46
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.27
Consensus pattern (15 bp):
TGAAACTATAGACTA
Found at i:17016070 original size:50 final size:50
Alignment explanation
Indices: 17015971--17016209 Score: 239
Period size: 50 Copynumber: 4.7 Consensus size: 50
17015961 AAAGAGATCT
* *
17015971 CATGTAAGACCATGTCTAGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAGGTCC
*
17016027 CATGTAAGACCATGTCTGGGACATGGCATTAGCACCGAGATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCC
** * * * **
17016077 CCCGTAAGACCATGTCTGGGATATGGCATGGGCACCGATATGAGAACTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCC
* * * * **
17016127 CATGTAAGACCATATCTGGGATATGGCATTGGCA--GTACATGAAACATCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAGAGGTCC
* *
17016176 CATGTAAGACCATGTCTAGGACATGGCTTTGGCA
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCA
17016210 TGTTATTATC
Statistics
Matches: 159, Mismatches: 23, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
48 1 0.01
49 39 0.25
50 83 0.52
53 3 0.02
55 1 0.01
56 32 0.20
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.23
Consensus pattern (50 bp):
CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCC
Found at i:17025522 original size:20 final size:20
Alignment explanation
Indices: 17025484--17025522 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
17025474 TACTTTCTTC
*
17025484 TTTACTTACTCTCTGACTTG
1 TTTACTTACTCTCTAACTTG
17025504 TTTACTTACT-TGCTAACTT
1 TTTACTTACTCT-CTAACTT
17025523 AAATAACACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.18, C:0.23, G:0.08, T:0.51
Consensus pattern (20 bp):
TTTACTTACTCTCTAACTTG
Found at i:17025825 original size:50 final size:50
Alignment explanation
Indices: 17025710--17025944 Score: 145
Period size: 50 Copynumber: 4.6 Consensus size: 50
17025700 TAATAACATG
* * ** * *
17025710 CCAAAGCCATGTCCCAAACATGGTCTTACATGG-GATGTTTCCTATAC--TA
1 CCAATGCCATGTCCCAGACATGGTCTTACA-GGAGACCTCTCATAT-CGGTA
* * * * ** *
17025759 CAAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACAGGAGACCTCTCATATCGGTA
* * * * *
17025809 CCCATGCCATGTCCCAGGCATGGTCTTACGGGGGACCTCTCATCTCGGTA
1 CCAATGCCATGTCCCAGACATGGTCTTACAGGAGACCTCTCATATCGGTA
* * * **
17025859 CCAACGCCATGTCCCAGACATGGTCTTA-TGTGGGACCTCTCATAAGCTCAATAA
1 CCAATGCCATGTCCCAGACATGGTCTTACAG-GAGACCTCTCAT-A--TCGGT-A
*
17025913 TGCCAATGCCATGTCCCAAACATGGTCTTACA
1 --CCAATGCCATGTCCCAGACATGGTCTTACA
17025945 TGGGGTCTCA
Statistics
Matches: 142, Mismatches: 33, Indels: 14
0.75 0.17 0.07
Matches are distributed among these distances:
48 2 0.01
49 34 0.24
50 76 0.54
53 3 0.02
54 1 0.01
56 26 0.18
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.26
Consensus pattern (50 bp):
CCAATGCCATGTCCCAGACATGGTCTTACAGGAGACCTCTCATATCGGTA
Found at i:17026325 original size:30 final size:30
Alignment explanation
Indices: 17026291--17026348 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
17026281 TCCTTGACTC
17026291 AAACTTTGGCAAATTTACAATTTTGCCCTT
1 AAACTTTGGCAAATTTACAATTTTGCCCTT
* * *
17026321 AAACTTTTGCATATTTACACTTTTGCCC
1 AAACTTTGGCAAATTTACAATTTTGCCC
17026349 CAAAGTTTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.28, C:0.22, G:0.09, T:0.41
Consensus pattern (30 bp):
AAACTTTGGCAAATTTACAATTTTGCCCTT
Found at i:17027473 original size:13 final size:14
Alignment explanation
Indices: 17027455--17027495 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
17027445 GATATAGATA
17027455 CAGATA-ACAAAAT
1 CAGATATACAAAAT
* *
17027468 CAGATATGCAGAAT
1 CAGATATACAAAAT
17027482 -AGATATACAAAAT
1 CAGATATACAAAAT
17027495 C
1 C
17027496 CTATCCCCCG
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
13 17 0.77
14 5 0.23
ACGTcount: A:0.54, C:0.15, G:0.12, T:0.20
Consensus pattern (14 bp):
CAGATATACAAAAT
Found at i:17037831 original size:48 final size:48
Alignment explanation
Indices: 17037760--17037904 Score: 281
Period size: 48 Copynumber: 3.0 Consensus size: 48
17037750 TCGAGAGGCC
17037760 AAGCAACTAAGAAACAAAAGTATTGCACTTGTGAAAGTATTATGGAAT
1 AAGCAACTAAGAAACAAAAGTATTGCACTTGTGAAAGTATTATGGAAT
17037808 AAGCAACTAAGAAACAAAAGTATTGCACTTGTGAAAGTATTATGGAAT
1 AAGCAACTAAGAAACAAAAGTATTGCACTTGTGAAAGTATTATGGAAT
*
17037856 AAGCAACTAAGAAACAAAAGTATTGCACTTGTGAAATTATTATGGAAT
1 AAGCAACTAAGAAACAAAAGTATTGCACTTGTGAAAGTATTATGGAAT
17037904 A
1 A
17037905 GGCATGGGGT
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
48 96 1.00
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.26
Consensus pattern (48 bp):
AAGCAACTAAGAAACAAAAGTATTGCACTTGTGAAAGTATTATGGAAT
Found at i:17044171 original size:50 final size:50
Alignment explanation
Indices: 17044081--17044253 Score: 145
Period size: 50 Copynumber: 3.5 Consensus size: 50
17044071 GAGGTCCCAC
* * * * * *
17044081 GTAAGACCATGTCTAGGACATGGCGTTGGTACTGAGATGAGAACT-TCCCT
1 GTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAACTCT-CAT
*
17044131 GTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCTCAT
1 GTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAACTCTCAT
* * * * ** ** * *
17044181 GTATGACCATATCTGGGATATGGAATTTGCA-ATACAGGA-AACATCTCAT
1 GTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAAC-TCTCAT
*
17044230 GTAATACCATGTCTGGGACATGGC
1 GTAAGACCATGTCTGGGACATGGC
17044254 TTTGGCATGT
Statistics
Matches: 99, Mismatches: 22, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
48 3 0.03
49 29 0.29
50 66 0.67
51 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.25
Consensus pattern (50 bp):
GTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAACTCTCAT
Found at i:17067458 original size:22 final size:22
Alignment explanation
Indices: 17067428--17067474 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
17067418 TTTGGTATTT
17067428 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
17067450 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
17067472 GGG
1 GGG
17067475 TTCAAAAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.32, C:0.04, G:0.40, T:0.23
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:17081270 original size:15 final size:15
Alignment explanation
Indices: 17081240--17081293 Score: 80
Period size: 14 Copynumber: 3.9 Consensus size: 15
17081230 CTAGCTTTTC
17081240 TTTTTTTT--CAAA-
1 TTTTTTTTCACAAAT
17081252 TTTTTTTTCACAAAT
1 TTTTTTTTCACAAAT
17081267 TTTTTTTTCA-AAAT
1 TTTTTTTTCACAAAT
17081281 TTTTTTTTCACAA
1 TTTTTTTTCACAA
17081294 CTTGATATCC
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
12 8 0.21
14 18 0.47
15 12 0.32
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTTTTTCACAAAT
Found at i:17081349 original size:13 final size:12
Alignment explanation
Indices: 17081331--17081374 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
17081321 TGGAAACTAG
*
17081331 TTTTTTTCGAAT
1 TTTTTTTTGAAT
17081343 TTTTTTTTGAAT
1 TTTTTTTTGAAT
*
17081355 TTTTTTTTGAGT
1 TTTTTTTTGAAT
17081367 TTTTTTTT
1 TTTTTTTT
17081375 CGAGAAACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.11, C:0.02, G:0.09, T:0.77
Consensus pattern (12 bp):
TTTTTTTTGAAT
Found at i:17084347 original size:27 final size:28
Alignment explanation
Indices: 17084317--17084535 Score: 240
Period size: 27 Copynumber: 8.1 Consensus size: 28
17084307 TTACACTGTT
* *
17084317 ATGATCAG-AATAGCCTCATAGGGTAAA
1 ATGATCAGAAATACCCCCATAGGGTAAA
*
17084344 ATGATC-GAAATACCCCCATAGGGTAGA
1 ATGATCAGAAATACCCCCATAGGGTAAA
** * *
17084371 ATGA-CCTAAATACCCCCAAAGGGTAGA
1 ATGATCAGAAATACCCCCATAGGGTAAA
* *
17084398 ATGACCA-AAATA-CCCCATAAGGTAAA
1 ATGATCAGAAATACCCCCATAGGGTAAA
* * *
17084424 ATAAT-TGAAATACCCCCATAGGGTAGA
1 ATGATCAGAAATACCCCCATAGGGTAAA
* *
17084451 ATGA-CGGAAATACCCCCATAAGGTAAA
1 ATGATCAGAAATACCCCCATAGGGTAAA
*
17084478 ATGACCA-AAATACCCCCATAGGGTAAA
1 ATGATCAGAAATACCCCCATAGGGTAAA
17084505 ATGATC-GAAATACCCCCATAGGGTAAA
1 ATGATCAGAAATACCCCCATAGGGTAAA
17084532 ATGA
1 ATGA
17084536 CTATTCTACC
Statistics
Matches: 163, Mismatches: 21, Indels: 16
0.81 0.10 0.08
Matches are distributed among these distances:
26 21 0.13
27 140 0.86
28 2 0.01
ACGTcount: A:0.42, C:0.21, G:0.18, T:0.18
Consensus pattern (28 bp):
ATGATCAGAAATACCCCCATAGGGTAAA
Found at i:17084481 original size:80 final size:81
Alignment explanation
Indices: 17084333--17084536 Score: 322
Period size: 80 Copynumber: 2.5 Consensus size: 81
17084323 AGAATAGCCT
* *
17084333 CATAGGGTAAAATGATCGAAATACCCCCATAGGGTAGAATGACCTAAATACCCCCAAAGGGTAGA
1 CATAGGGTAAAATGATCGAAATACCCCCATAGGGTAGAATGACCGAAATACCCCCAAAGGGTAAA
17084398 ATGACCAAAATA-CCC
66 ATGACCAAAATACCCC
* * * *
17084413 CATAAGGTAAAATAATTGAAATACCCCCATAGGGTAGAATGACGGAAATACCCCCATAA-GGTAA
1 CATAGGGTAAAATGATCGAAATACCCCCATAGGGTAGAATGACCGAAATACCCCCA-AAGGGTAA
17084477 AATGACCAAAATACCCC
65 AATGACCAAAATACCCC
*
17084494 CATAGGGTAAAATGATCGAAATACCCCCATAGGGTAAAATGAC
1 CATAGGGTAAAATGATCGAAATACCCCCATAGGGTAGAATGAC
17084537 TATTCTACCC
Statistics
Matches: 112, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
80 68 0.61
81 44 0.39
ACGTcount: A:0.43, C:0.22, G:0.18, T:0.17
Consensus pattern (81 bp):
CATAGGGTAAAATGATCGAAATACCCCCATAGGGTAGAATGACCGAAATACCCCCAAAGGGTAAA
ATGACCAAAATACCCC
Found at i:17084492 original size:54 final size:54
Alignment explanation
Indices: 17084333--17084536 Score: 268
Period size: 54 Copynumber: 3.8 Consensus size: 54
17084323 AGAATAGCCT
* * *
17084333 CATAGGGTAAAATGATCGAAATACCCCCATAGGGTAGAATGACCTAAATACCCC
1 CATAGGGTAAAATGATCGAAATACCCCCATAAGGTAAAATGACCAAAATACCCC
* * * * * ***
17084387 CAAAGGGTAGAATGACCAAAATA-CCCCATAAGGTAAAATAATTGAAATACCCC
1 CATAGGGTAAAATGATCGAAATACCCCCATAAGGTAAAATGACCAAAATACCCC
*
17084440 CATAGGGTAGAATGA-CGGAAATACCCCCATAAGGTAAAATGACCAAAATACCCC
1 CATAGGGTAAAATGATC-GAAATACCCCCATAAGGTAAAATGACCAAAATACCCC
*
17084494 CATAGGGTAAAATGATCGAAATACCCCCATAGGGTAAAATGAC
1 CATAGGGTAAAATGATCGAAATACCCCCATAAGGTAAAATGAC
17084537 TATTCTACCC
Statistics
Matches: 129, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
52 1 0.01
53 43 0.33
54 84 0.65
55 1 0.01
ACGTcount: A:0.43, C:0.22, G:0.18, T:0.17
Consensus pattern (54 bp):
CATAGGGTAAAATGATCGAAATACCCCCATAAGGTAAAATGACCAAAATACCCC
Found at i:17087318 original size:27 final size:27
Alignment explanation
Indices: 17087287--17087646 Score: 391
Period size: 27 Copynumber: 13.4 Consensus size: 27
17087277 ACTCCATAGA
*
17087287 GTAAAATGACCAAAATACCCCCATAAG
1 GTAAAATGACCGAAATACCCCCATAAG
* * * *
17087314 GTAAAATAATCAAAATCCCCCCAT-AG
1 GTAAAATGACCGAAATACCCCCATAAG
* * * *
17087340 GATAGAATGACTGAAATATCCCCATACG
1 G-TAAAATGACCGAAATACCCCCATAAG
* *
17087368 GTAAAATGATCGAAATACCCCCAGAAG
1 GTAAAATGACCGAAATACCCCCATAAG
* * * *
17087395 GTAGAATGATCGAAATACTCCCATAGG
1 GTAAAATGACCGAAATACCCCCATAAG
*
17087422 GTAGAATGACCGAAATACCCCCATAAG
1 GTAAAATGACCGAAATACCCCCATAAG
* *
17087449 GTAAAATGAGCGAAATACCCCCATATG
1 GTAAAATGACCGAAATACCCCCATAAG
* * *
17087476 GTAAAATGATCGAAATACCCTCATAGG
1 GTAAAATGACCGAAATACCCCCATAAG
* * *
17087503 GTAAATTGACCGAAATACCCTCATAGG
1 GTAAAATGACCGAAATACCCCCATAAG
* * *
17087530 GTAAAATGATCGAAATACCCTCATAAA
1 GTAAAATGACCGAAATACCCCCATAAG
* *
17087557 GTAAAATGACCGAAATACCTCCATAGG
1 GTAAAATGACCGAAATACCCCCATAAG
* *
17087584 GTAAACTAACCGAAATACCCCCATAAG
1 GTAAAATGACCGAAATACCCCCATAAG
* * *
17087611 GTAGATTGACCGAAATA-CCCCATAGG
1 GTAAAATGACCGAAATACCCCCATAAG
17087637 GTAAAATGAC
1 GTAAAATGAC
17087647 TGTTATACCC
Statistics
Matches: 280, Mismatches: 51, Indels: 5
0.83 0.15 0.01
Matches are distributed among these distances:
26 19 0.07
27 259 0.93
28 2 0.01
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.19
Consensus pattern (27 bp):
GTAAAATGACCGAAATACCCCCATAAG
Found at i:17087374 original size:81 final size:81
Alignment explanation
Indices: 17087287--17087645 Score: 436
Period size: 81 Copynumber: 4.4 Consensus size: 81
17087277 ACTCCATAGA
* * * * *
17087287 GTAAAATGACCAAAATACCCCCATAAGGTAAAATAATCAAAATCCCCCCATAGGATAGAA-TGAC
1 GTAAAATGACCGAAATACCCCCATAAGGTAAAATGATCGAAATACCCCCATAGGGTA-AACTGAC
* * *
17087351 TGAAATATCCCCATACG
65 CGAAATACCCCCATAAG
* * * *
17087368 GTAAAATGATCGAAATACCCCCAGAAGGTAGAATGATCGAAATACTCCCATAGGGTAGAA-TGAC
1 GTAAAATGACCGAAATACCCCCATAAGGTAAAATGATCGAAATACCCCCATAGGGTA-AACTGAC
17087432 CGAAATACCCCCATAAG
65 CGAAATACCCCCATAAG
* * * *
17087449 GTAAAATGAGCGAAATACCCCCATATGGTAAAATGATCGAAATACCCTCATAGGGTAAATTGACC
1 GTAAAATGACCGAAATACCCCCATAAGGTAAAATGATCGAAATACCCCCATAGGGTAAACTGACC
* *
17087514 GAAATACCCTCATAGG
66 GAAATACCCCCATAAG
* * * * * *
17087530 GTAAAATGATCGAAATACCCTCATAAAGTAAAATGACCGAAATACCTCCATAGGGTAAACTAACC
1 GTAAAATGACCGAAATACCCCCATAAGGTAAAATGATCGAAATACCCCCATAGGGTAAACTGACC
17087595 GAAATACCCCCATAAG
66 GAAATACCCCCATAAG
* * *
17087611 GTAGATTGACCGAAATA-CCCCATAGGGTAAAATGA
1 GTAAAATGACCGAAATACCCCCATAAGGTAAAATGA
17087646 CTGTTATACC
Statistics
Matches: 240, Mismatches: 37, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
80 17 0.07
81 223 0.93
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.19
Consensus pattern (81 bp):
GTAAAATGACCGAAATACCCCCATAAGGTAAAATGATCGAAATACCCCCATAGGGTAAACTGACC
GAAATACCCCCATAAG
Found at i:17096253 original size:16 final size:15
Alignment explanation
Indices: 17096221--17096259 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
17096211 TGATAATAAC
17096221 TAATATATAATTATAT
1 TAAT-TATAATTATAT
*
17096237 TTATTATAATGTATAT
1 TAATTATAAT-TATAT
17096253 TAATTAT
1 TAATTAT
17096260 TATCAACTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (15 bp):
TAATTATAATTATAT
Found at i:17104093 original size:12 final size:12
Alignment explanation
Indices: 17104076--17104132 Score: 69
Period size: 12 Copynumber: 4.8 Consensus size: 12
17104066 TTGTAGATTC
17104076 AAAAAAAATCAA
1 AAAAAAAATCAA
*
17104088 AAAAAAAATCGA
1 AAAAAAAATCAA
* *
17104100 AAAAAAATTGAA
1 AAAAAAAATCAA
* *
17104112 AAAAAAATTGAA
1 AAAAAAAATCAA
17104124 AAAAAAAAT
1 AAAAAAAAT
17104133 TACATACGGT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 40 1.00
ACGTcount: A:0.79, C:0.04, G:0.05, T:0.12
Consensus pattern (12 bp):
AAAAAAAATCAA
Found at i:17104106 original size:23 final size:23
Alignment explanation
Indices: 17104076--17104129 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
17104066 TTGTAGATTC
17104076 AAAAAAAATCAAAAAAAAAATCG
1 AAAAAAAATCAAAAAAAAAATCG
** *
17104099 AAAAAAAATTGAAAAAAAAATTG
1 AAAAAAAATCAAAAAAAAAATCG
17104122 AAAAAAAA
1 AAAAAAAA
17104130 AATTACATAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.80, C:0.04, G:0.06, T:0.11
Consensus pattern (23 bp):
AAAAAAAATCAAAAAAAAAATCG
Found at i:17120373 original size:24 final size:23
Alignment explanation
Indices: 17120319--17120374 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 23
17120309 GGATAACTAA
* *
17120319 GAAAGGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGATTTGGTAC
***
17120342 GTTTTGGTATTTGGGATTTGGTAC
1 GAAATGGTATTT-GGATTTGGTAC
17120366 GAAATGGTA
1 GAAATGGTA
17120375 ATGGTTCAAA
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
23 8 0.33
24 16 0.67
ACGTcount: A:0.21, C:0.04, G:0.34, T:0.41
Consensus pattern (23 bp):
GAAATGGTATTTGGATTTGGTAC
Found at i:17126910 original size:16 final size:16
Alignment explanation
Indices: 17126889--17126922 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
17126879 TAAATAAGCT
*
17126889 TAATAAAATCCCAAAA
1 TAATAAAATACCAAAA
17126905 TAATAAAATACCAAAA
1 TAATAAAATACCAAAA
17126921 TA
1 TA
17126923 TAGTTGAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.65, C:0.15, G:0.00, T:0.21
Consensus pattern (16 bp):
TAATAAAATACCAAAA
Found at i:17127488 original size:21 final size:21
Alignment explanation
Indices: 17127424--17127491 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
17127414 TTGTTAGATA
* *
17127424 CAGATATTGTGGACAAGCCAC
1 CAGAAATTGTGGATAAGCCAC
* * *
17127445 CA-AATATTGTAGATAAACTAC
1 CAGAA-ATTGTGGATAAGCCAC
*
17127466 CAGAAATTGTGGTTAAGCCAC
1 CAGAAATTGTGGATAAGCCAC
17127487 CAGAA
1 CAGAA
17127492 TGTTCAGATC
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
20 1 0.03
21 33 0.92
22 2 0.06
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (21 bp):
CAGAAATTGTGGATAAGCCAC
Found at i:17128430 original size:22 final size:22
Alignment explanation
Indices: 17128390--17128444 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
17128380 ACAACTCCAA
* *
17128390 AATCACCACCCTACCACCACCG
1 AATCACCACCATACAACCACCG
*
17128412 AATCACCACCATTCAACCACCG
1 AATCACCACCATACAACCACCG
* *
17128434 TAGCACCACCA
1 AATCACCACCA
17128445 CACCTCTACC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.49, G:0.05, T:0.11
Consensus pattern (22 bp):
AATCACCACCATACAACCACCG
Found at i:17132944 original size:16 final size:16
Alignment explanation
Indices: 17132923--17132964 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
17132913 ATTAGAATCT
17132923 TTACTCGCTTCTTTAC
1 TTACTCGCTTCTTTAC
* *
17132939 TTACTCACTTGTTTAC
1 TTACTCGCTTCTTTAC
*
17132955 TTACTTGCTT
1 TTACTCGCTT
17132965 ACTTAAATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.14, C:0.26, G:0.07, T:0.52
Consensus pattern (16 bp):
TTACTCGCTTCTTTAC
Found at i:17133838 original size:16 final size:16
Alignment explanation
Indices: 17133817--17133858 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
17133807 ATTAGAATCT
17133817 TTACTCGCTTCTTTAC
1 TTACTCGCTTCTTTAC
* *
17133833 TTACTCACTTGTTTAC
1 TTACTCGCTTCTTTAC
*
17133849 TTACTTGCTT
1 TTACTCGCTT
17133859 ACTTAAATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.14, C:0.26, G:0.07, T:0.52
Consensus pattern (16 bp):
TTACTCGCTTCTTTAC
Found at i:17133890 original size:894 final size:895
Alignment explanation
Indices: 17132161--17133952 Score: 3487
Period size: 894 Copynumber: 2.0 Consensus size: 895
17132151 TAAAGTCTCC
17132161 CCTATTTCACTGCCTGATGGTTCTGACCTTTATTCACTAAAAATCAATTTTCTCATCATATGATT
1 CCTATTTCACTGCCTGATGGTTCTGACCTTTATTCACTAAAAATCAATTTTCTCATCATATGATT
17132226 TTCATATGGTGTTCTCACTTGTTTCTACAAAAAATAGACTCACTAAAGAATCTGAAAATTTAAAT
66 TTCATATGGTGTTCTCACTTGTTTCTACAAAAAATAGACTCACTAAAGAATCTGAAAATTTAAAT
*
17132291 TATAGCTCATAACCATTTTTTTTTAAAATTTTTAATGATTTTCTAAAGTCAGAACATGGGACTTC
131 TATAGCTCATAACCATTTTTTTTAAAAATTTTTAATGATTTTCTAAAGTCAGAACATGGGACTTC
17132356 AAAAACCATTCTAAACCTATCTAACCAAAATTCAAATATCTCAGAGTATAAAACTTCTTTACCCA
196 AAAAACCATTCTAAACCTATCTAACCAAAATTCAAATATCTCAGAGTATAAAACTTCTTTACCCA
17132421 CAATGTTATTTTTCTATGAAAATAGACTAGATAAGCTTTAATTATATATATCATTCACTCTCTAA
261 CAATGTTATTTTTCTATGAAAATAGACTAGATAAGCTTTAATTATATATATCATTCACTCTCTAA
17132486 TTCGTTTTATACTATCCTTGGTGATTTTTCAAAGTCACGTCACTGCTGCTGTCCCAAAACTGTTT
326 TTCGTTTTATACTATCCTTGGTGATTTTTCAAAGTCACGTCACTGCTGCTGTCCCAAAACTGTTT
17132551 CATTGCAAATTTTTATTCTCCTTCATAATTTTAAGGTATAAACTATCACCTAGGCATTCATAACA
391 CATTGCAAATTTTTATTCTCCTTCATAATTTTAAGGTATAAACTATCACCTAGGCATTCATAACA
17132616 CCACACATGTTCTTAATTAGCCATTTCAATAGCTAATAATTAGCCACATCATATAAACACACACA
456 CCACACATGTTCTTAATTAGCCATTTCAATAGCTAATAATTAGCCACATCATATAAACACACACA
*
17132681 AAATTACTAAGTCTCTATACATGCCATAGCTTTACACGTTTCAAAATCACATACTACCGAGATGT
521 AAATTACTAAGTATCTATACATGCCATAGCTTTACACGTTTCAAAATCACATACTACCGAGATGT
17132746 CTGCTGATAGTGTGAGACGAACTCTGACGTCCTTGTGATCCTCGAACTGACTTGTCGATACTATA
586 CTGCTGATAGTGTGAGACGAACTCTGACGTCCTTGTGATCCTCGAACTGACTTGTCGATACTATA
17132811 AAAATAAAAAATATAGAAACTAAGCATAAAGCTTAGTAAGTTTACAAGTAAATAAATAAAAACAT
651 AAAATAAAAAATATAGAAACTAAGCATAAAGCTTAGTAAGTTTACAAGTAAATAAATAAAAACAT
*
17132876 TTATTATATATAATCATACTCATAAATTTCATCAAACATTAGAATCTTTACTCGCTTCTTTACTT
716 TTATTATATATAATCATACTAATAAATTTCATCAAACATTAGAATCTTTACTCGCTTCTTTACTT
*
17132941 ACTCACTTGTTTACTTACTTGCTTACTTAAATAACTCATAATTATAACTTACTCCTCCCTTGCTG
781 ACTCACTTGTTTACTTACTTGCTTACTTAAATAACTCATAATTATAACTTACTCCTCCCTTGCTA
17133006 AAATTTCTTTCTCAATTGATAACTCTGATATTCTCAATCCTTATAACTCA
846 AAATTTCTTTCTCAATTGATAACTCTGATATTCTCAATCCTTATAACTCA
17133056 CCTATTTCACTGCCTGATGGTTCTGACCTTTATTCACTAAAAATCAATTTTCTCATCATATGATT
1 CCTATTTCACTGCCTGATGGTTCTGACCTTTATTCACTAAAAATCAATTTTCTCATCATATGATT
17133121 TTCATATGGTGTTCTCACTTGTTTCTACAAAAAATAGACTCACTAAAGAATCTGAAAATTTAAAT
66 TTCATATGGTGTTCTCACTTGTTTCTACAAAAAATAGACTCACTAAAGAATCTGAAAATTTAAAT
17133186 TATAGCTCATAACCA-TTTTTTTAAAAATTTTTAATGATTTTCTAAAGTCAGAACATGGGACTTC
131 TATAGCTCATAACCATTTTTTTTAAAAATTTTTAATGATTTTCTAAAGTCAGAACATGGGACTTC
*
17133250 AAAAACCATTCTAACCCTATCTAACCAAAATTCAAATATCTCAGAGTATAAAACTTCTTTACCCA
196 AAAAACCATTCTAAACCTATCTAACCAAAATTCAAATATCTCAGAGTATAAAACTTCTTTACCCA
17133315 CAATGTTATTTTTCTATGAAAATAGACTAGATAAGCTTTAATTATATATATCATTCACTCTCTAA
261 CAATGTTATTTTTCTATGAAAATAGACTAGATAAGCTTTAATTATATATATCATTCACTCTCTAA
*
17133380 TTCGTTTTATACTATCCTTGGTGATTTTTCAAATTCACGTCACTGCTGCTGTCCCAAAACTGTTT
326 TTCGTTTTATACTATCCTTGGTGATTTTTCAAAGTCACGTCACTGCTGCTGTCCCAAAACTGTTT
17133445 CATTGCAAATTTTTATTCTCCTTCATAATTTTAAGGTATAAACTATCACCTAGGCATTCATAACA
391 CATTGCAAATTTTTATTCTCCTTCATAATTTTAAGGTATAAACTATCACCTAGGCATTCATAACA
*
17133510 CCACACATGTTCTTAATTAGCCATTTCAATAGCTAATAATTAGCCACATCATATAAACACACTCA
456 CCACACATGTTCTTAATTAGCCATTTCAATAGCTAATAATTAGCCACATCATATAAACACACACA
*
17133575 AAATTACTAAGTATCTATACATGCCATAGCTTTACACGTTTCGAAATCACATACTACCGAGATGT
521 AAATTACTAAGTATCTATACATGCCATAGCTTTACACGTTTCAAAATCACATACTACCGAGATGT
17133640 CTGCTGATAGTGTGAGACGAACTCTGACGTCCTTGTGATCCTCGAACTGACTTGTCGATACTATA
586 CTGCTGATAGTGTGAGACGAACTCTGACGTCCTTGTGATCCTCGAACTGACTTGTCGATACTATA
* *
17133705 AAAATAAAAAATATAGAAAGTAAGCATAAAGCTTAGTAAGTTTACAAGTAAATAAATAACAACAT
651 AAAATAAAAAATATAGAAACTAAGCATAAAGCTTAGTAAGTTTACAAGTAAATAAATAAAAACAT
17133770 TTATTATATATAATCATACTAATAAATTTCATCAAACATTAGAATCTTTACTCGCTTCTTTACTT
716 TTATTATATATAATCATACTAATAAATTTCATCAAACATTAGAATCTTTACTCGCTTCTTTACTT
17133835 ACTCACTTGTTTACTTACTTGCTTACTTAAATAACTCATAATTATAACTTACTCCTCCCTTGCTA
781 ACTCACTTGTTTACTTACTTGCTTACTTAAATAACTCATAATTATAACTTACTCCTCCCTTGCTA
17133900 AAATTTCTTTCTCAATTGATAACTCTGATATTCTCAATCCTTATAACTCA
846 AAATTTCTTTCTCAATTGATAACTCTGATATTCTCAATCCTTATAACTCA
17133950 CCT
1 CCT
17133953 GAATTTATTA
Statistics
Matches: 887, Mismatches: 10, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
894 742 0.84
895 145 0.16
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.36
Consensus pattern (895 bp):
CCTATTTCACTGCCTGATGGTTCTGACCTTTATTCACTAAAAATCAATTTTCTCATCATATGATT
TTCATATGGTGTTCTCACTTGTTTCTACAAAAAATAGACTCACTAAAGAATCTGAAAATTTAAAT
TATAGCTCATAACCATTTTTTTTAAAAATTTTTAATGATTTTCTAAAGTCAGAACATGGGACTTC
AAAAACCATTCTAAACCTATCTAACCAAAATTCAAATATCTCAGAGTATAAAACTTCTTTACCCA
CAATGTTATTTTTCTATGAAAATAGACTAGATAAGCTTTAATTATATATATCATTCACTCTCTAA
TTCGTTTTATACTATCCTTGGTGATTTTTCAAAGTCACGTCACTGCTGCTGTCCCAAAACTGTTT
CATTGCAAATTTTTATTCTCCTTCATAATTTTAAGGTATAAACTATCACCTAGGCATTCATAACA
CCACACATGTTCTTAATTAGCCATTTCAATAGCTAATAATTAGCCACATCATATAAACACACACA
AAATTACTAAGTATCTATACATGCCATAGCTTTACACGTTTCAAAATCACATACTACCGAGATGT
CTGCTGATAGTGTGAGACGAACTCTGACGTCCTTGTGATCCTCGAACTGACTTGTCGATACTATA
AAAATAAAAAATATAGAAACTAAGCATAAAGCTTAGTAAGTTTACAAGTAAATAAATAAAAACAT
TTATTATATATAATCATACTAATAAATTTCATCAAACATTAGAATCTTTACTCGCTTCTTTACTT
ACTCACTTGTTTACTTACTTGCTTACTTAAATAACTCATAATTATAACTTACTCCTCCCTTGCTA
AAATTTCTTTCTCAATTGATAACTCTGATATTCTCAATCCTTATAACTCA
Found at i:17135730 original size:13 final size:13
Alignment explanation
Indices: 17135714--17135745 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
17135704 AAAGAGTTCG
17135714 AAAAAAAAATTGA
1 AAAAAAAAATTGA
17135727 AAAAAAAAATTGA
1 AAAAAAAAATTGA
17135740 AAAAAA
1 AAAAAA
17135746 GAAAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.12
Consensus pattern (13 bp):
AAAAAAAAATTGA
Found at i:17136874 original size:18 final size:18
Alignment explanation
Indices: 17136853--17136890 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
17136843 AAAGCAAAAA
17136853 GAGATTGA-AAAAGAAATT
1 GAGATTGAGAAAA-AAATT
17136871 GAGATTGAGAAAAAAATT
1 GAGATTGAGAAAAAAATT
17136889 GA
1 GA
17136891 AAAAGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.55, C:0.00, G:0.24, T:0.21
Consensus pattern (18 bp):
GAGATTGAGAAAAAAATT
Found at i:17140876 original size:50 final size:50
Alignment explanation
Indices: 17140815--17141052 Score: 325
Period size: 50 Copynumber: 4.8 Consensus size: 50
17140805 TACTGCTAAT
* * ** * *
17140815 GCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATAC-CGGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-CTCGGTGCCAAC
** *
17140865 GCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCAGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAC
**
17140915 GCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAC
* * * *
17140965 GCCATGTCCTAGACATGGTCTTACATGAGACCTCTCTTCTCGGAGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAC
17141015 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT
17141053 AATCTCAATG
Statistics
Matches: 168, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
49 1 0.01
50 167 0.99
ACGTcount: A:0.21, C:0.32, G:0.23, T:0.25
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAC
Found at i:17142650 original size:40 final size:40
Alignment explanation
Indices: 17142567--17142869 Score: 405
Period size: 40 Copynumber: 7.6 Consensus size: 40
17142557 TTGAATGCTG
* * * * * *
17142567 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
17142607 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
17142647 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
17142687 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
17142727 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
17142767 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
17142807 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
17142846 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
17142870 TGAACGAGGA
Statistics
Matches: 241, Mismatches: 19, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
39 35 0.15
40 198 0.82
41 8 0.03
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:17159103 original size:23 final size:22
Alignment explanation
Indices: 17159051--17159103 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
17159041 TCCACGTCTT
*
17159051 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
17159073 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
17159096 TTTCTTTT
1 TTTCTTTT
17159104 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:17163545 original size:21 final size:21
Alignment explanation
Indices: 17163501--17163557 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
17163491 CCATTACCAA
*
17163501 TTCGTACCAAATACCATAACAT
1 TTCGTACC-AATTCCATAACAT
17163523 TTCGTACCAATTCCAT-ACAAT
1 TTCGTACCAATTCCATAAC-AT
* *
17163544 TTTGAACCAATTCC
1 TTCGTACCAATTCC
17163558 CAAATACCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.06
21 21 0.68
22 8 0.26
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.32
Consensus pattern (21 bp):
TTCGTACCAATTCCATAACAT
Found at i:17178661 original size:13 final size:13
Alignment explanation
Indices: 17178643--17178667 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17178633 TGGTCATCAT
17178643 GGTGTGAACACAA
1 GGTGTGAACACAA
17178656 GGTGTGAACACA
1 GGTGTGAACACA
17178668 TGATCAATAC
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:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:17181121 original size:12 final size:12
Alignment explanation
Indices: 17181104--17181139 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 12
17181094 TAGCTCTCTC
17181104 TTTTTTTCAATT
1 TTTTTTTCAATT
17181116 TTTTTTTCACAATT
1 TTTTTTT--CAATT
17181130 TTTTTTTCAA
1 TTTTTTTCAA
17181140 AATTTTTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 10 0.45
14 12 0.55
ACGTcount: A:0.19, C:0.11, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTTTTCAATT
Found at i:17181128 original size:14 final size:14
Alignment explanation
Indices: 17181111--17181146 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
17181101 CTCTTTTTTT
17181111 CAATTTTTTTTTCA
1 CAATTTTTTTTTCA
17181125 CAATTTTTTTTTCA
1 CAATTTTTTTTTCA
*
17181139 AAATTTTT
1 CAATTTTT
17181147 GATCGCATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.25, C:0.11, G:0.00, T:0.64
Consensus pattern (14 bp):
CAATTTTTTTTTCA
Found at i:17181145 original size:12 final size:12
Alignment explanation
Indices: 17181104--17181146 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
17181094 TAGCTCTCTC
*
17181104 TTTTTTTCAATT
1 TTTTTTTCAAAT
17181116 TTTTTTTCACAATT
1 TTTTTTTCA-AA-T
*
17181130 TTTTTTTCAAAA
1 TTTTTTTCAAAT
17181142 TTTTT
1 TTTTT
17181147 GATCGCATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 14 0.52
13 3 0.11
14 10 0.37
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTTTTTCAAAT
Found at i:17193447 original size:11 final size:12
Alignment explanation
Indices: 17193404--17193447 Score: 72
Period size: 12 Copynumber: 3.7 Consensus size: 12
17193394 CAAGTTGTGA
17193404 AAAAAAAATTTG
1 AAAAAAAATTTG
17193416 AAAAAAAATTGTG
1 AAAAAAAATT-TG
17193429 AAAAAAAA-TTG
1 AAAAAAAATTTG
17193440 AAAAAAAA
1 AAAAAAAA
17193448 AGAGAGCTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.32
12 11 0.35
13 10 0.32
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (12 bp):
AAAAAAAATTTG
Found at i:17193448 original size:13 final size:13
Alignment explanation
Indices: 17193401--17193448 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
17193391 TACCAAGTTG
*
17193401 TGAAAAAAAAATT
1 TGAAAAAAAAAAT
17193414 TG--AAAAAAAAT
1 TGAAAAAAAAAAT
**
17193425 TGTGAAAAAAAAT
1 TGAAAAAAAAAAT
17193438 TGAAAAAAAAA
1 TGAAAAAAAAA
17193449 GAGAGCTAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 10 0.33
13 20 0.67
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (13 bp):
TGAAAAAAAAAAT
Found at i:17193448 original size:26 final size:26
Alignment explanation
Indices: 17193398--17193447 Score: 86
Period size: 24 Copynumber: 2.0 Consensus size: 26
17193388 GGATACCAAG
17193398 TTGTGAAAAAAAAATTTGAAAAAAAA
1 TTGTGAAAAAAAAATTTGAAAAAAAA
17193424 TTGTG-AAAAAAAA-TTGAAAAAAAA
1 TTGTGAAAAAAAAATTTGAAAAAAAA
17193448 AGAGAGCTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 11 0.46
25 8 0.33
26 5 0.21
ACGTcount: A:0.66, C:0.00, G:0.12, T:0.22
Consensus pattern (26 bp):
TTGTGAAAAAAAAATTTGAAAAAAAA
Found at i:17198789 original size:45 final size:45
Alignment explanation
Indices: 17198738--17198970 Score: 387
Period size: 45 Copynumber: 5.2 Consensus size: 45
17198728 TCGGCCATGG
* * *
17198738 TGCTTCCTCAATTTGTTCCATAAATTATGCATGATGTTGG-CTAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTC-AAA
*
17198783 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
17198828 TGCTTCCTCAAATTCTTCCATGAATTATGCATAATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
17198873 TGCTTCCTCAAATTCTCCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
17198918 TGCTTCCTCAAATTCTCCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
17198963 TGCTTCCT
1 TGCTTCCT
17198971 TAATTTCATG
Statistics
Matches: 179, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
45 178 0.99
46 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
Found at i:17204595 original size:56 final size:56
Alignment explanation
Indices: 17204511--17204628 Score: 218
Period size: 56 Copynumber: 2.1 Consensus size: 56
17204501 TTCCAGACTC
*
17204511 TTTTTTTTTGCGGATCTTTCACGTTCTTTTCGTCCGCGCCTAGACCGTAGGAAATT
1 TTTTTTTTTGAGGATCTTTCACGTTCTTTTCGTCCGCGCCTAGACCGTAGGAAATT
*
17204567 TTTTTTTTTGAGGATCTTTCACGTTCTTTTCGTCCGCGCCTAGACCGTAGGCAATT
1 TTTTTTTTTGAGGATCTTTCACGTTCTTTTCGTCCGCGCCTAGACCGTAGGAAATT
17204623 TTTTTT
1 TTTTTT
17204629 ATTTTTTTTA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 60 1.00
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (56 bp):
TTTTTTTTTGAGGATCTTTCACGTTCTTTTCGTCCGCGCCTAGACCGTAGGAAATT
Found at i:17205249 original size:45 final size:45
Alignment explanation
Indices: 17205200--17205432 Score: 394
Period size: 45 Copynumber: 5.2 Consensus size: 45
17205190 TCGGCCATGG
* * * * *
17205200 TGCTTCCTCAATTTGTTTCATAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
17205245 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
17205290 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
17205335 TGCTTCCTCAAATTCTCCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
17205380 TGCTTCCTCAAATTCTCCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
17205425 TGCTTCCT
1 TGCTTCCT
17205433 TAATTTCATG
Statistics
Matches: 180, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 180 1.00
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
Found at i:17206079 original size:30 final size:30
Alignment explanation
Indices: 17206045--17206141 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
17206035 AGCTCACTCC
17206045 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
17206075 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
17206105 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
17206135 TAGCTCA
1 TAGCTCA
17206142 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:17209758 original size:18 final size:18
Alignment explanation
Indices: 17209735--17209770 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
17209725 AGATTAAAAA
17209735 AATCAGA-TCACAAAGAAT
1 AATCAGATTCA-AAAGAAT
17209753 AATCAGATTCAAAAGAAT
1 AATCAGATTCAAAAGAAT
17209771 TCTAGGGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.56, C:0.14, G:0.11, T:0.19
Consensus pattern (18 bp):
AATCAGATTCAAAAGAAT
Found at i:17214775 original size:23 final size:23
Alignment explanation
Indices: 17214731--17214775 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
17214721 TGAAATCGAC
17214731 ACAAGCAGAAAATTAAAAAGATTG
1 ACAAGCAGAAAA-TAAAAAGATTG
17214755 ACAAGCAAGAAAA-AAAAAGAT
1 ACAAGC-AGAAAATAAAAAGAT
17214776 AAAGTCCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 8 0.40
24 6 0.30
25 6 0.30
ACGTcount: A:0.64, C:0.09, G:0.16, T:0.11
Consensus pattern (23 bp):
ACAAGCAGAAAATAAAAAGATTG
Found at i:17220769 original size:20 final size:20
Alignment explanation
Indices: 17220739--17220793 Score: 101
Period size: 20 Copynumber: 2.7 Consensus size: 20
17220729 TCGAATTAGC
17220739 TCAACTTCAGCTCAAACATTT
1 TCAA-TTCAGCTCAAACATTT
17220760 TCAATTCAGCTCAAACATTT
1 TCAATTCAGCTCAAACATTT
17220780 TCAATTCAGCTCAA
1 TCAATTCAGCTCAA
17220794 TATCAACTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 30 0.88
21 4 0.12
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.33
Consensus pattern (20 bp):
TCAATTCAGCTCAAACATTT
Found at i:17222230 original size:13 final size:12
Alignment explanation
Indices: 17222214--17222246 Score: 57
Period size: 12 Copynumber: 2.7 Consensus size: 12
17222204 AAAGAGTTCG
17222214 AAAAAAAATTGA
1 AAAAAAAATTGA
17222226 AAAAAAAATTGA
1 AAAAAAAATTGA
17222238 AAAGAAAAA
1 AAA-AAAAA
17222247 AAAAATTGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (12 bp):
AAAAAAAATTGA
Found at i:17223065 original size:15 final size:15
Alignment explanation
Indices: 17223033--17223066 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
17223023 GTTCAACGAA
*
17223033 GAGGCCAACGCAACC
1 GAGGCCAACGAAACC
*
17223048 GAGGCCAACGAAATC
1 GAGGCCAACGAAACC
17223063 GAGG
1 GAGG
17223067 GAGGTTCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.32, T:0.03
Consensus pattern (15 bp):
GAGGCCAACGAAACC
Found at i:17243865 original size:29 final size:27
Alignment explanation
Indices: 17243832--17243886 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
17243822 GTGATTAAAT
17243832 AAAATCGACA-CAAGCAGAATTTAAAAGAA
1 AAAATCGACAGCAAG-A-AA-TTAAAAGAA
*
17243861 AAAATTGACAGCAAGAAATTAAAAGA
1 AAAATCGACAGCAAGAAATTAAAAGA
17243887 TAAGTCCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 8 0.33
28 2 0.08
29 10 0.42
30 4 0.17
ACGTcount: A:0.60, C:0.11, G:0.15, T:0.15
Consensus pattern (27 bp):
AAAATCGACAGCAAGAAATTAAAAGAA
Found at i:17248498 original size:19 final size:17
Alignment explanation
Indices: 17248462--17248500 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
17248452 TCAATTGCTG
17248462 ATTAGTTAAATAAATTA
1 ATTAGTTAAATAAATTA
*
17248479 ATTAGCTTAAGATTAATTA
1 ATTAG-TTAA-ATAAATTA
17248498 ATT
1 ATT
17248501 TAATAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 4 0.21
19 10 0.53
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (17 bp):
ATTAGTTAAATAAATTA
Found at i:17250783 original size:18 final size:18
Alignment explanation
Indices: 17250746--17250784 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
17250736 AACAAAAAAG
* *
17250746 AAGAAAAAGAAATTGTAA
1 AAGAAAAAGAAATCGAAA
17250764 AAGAAAAAGAAATCGAAA
1 AAGAAAAAGAAATCGAAA
17250782 AAG
1 AAG
17250785 TGAGAGAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.69, C:0.03, G:0.18, T:0.10
Consensus pattern (18 bp):
AAGAAAAAGAAATCGAAA
Found at i:17256295 original size:13 final size:13
Alignment explanation
Indices: 17256277--17256325 Score: 75
Period size: 13 Copynumber: 3.9 Consensus size: 13
17256267 TTGTAGATTC
*
17256277 AAAAAAAAATCGA
1 AAAAAAAAATTGA
17256290 AAAAAAAAATTG-
1 AAAAAAAAATTGA
17256302 -AAAAAAAATTGA
1 AAAAAAAAATTGA
17256314 AAAAAAAAATTG
1 AAAAAAAAATTG
17256326 CATACGGTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
11 11 0.33
13 22 0.67
ACGTcount: A:0.76, C:0.02, G:0.08, T:0.14
Consensus pattern (13 bp):
AAAAAAAAATTGA
Found at i:17256305 original size:10 final size:11
Alignment explanation
Indices: 17256291--17256320 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
17256281 AAAAATCGAA
17256291 AAAAAAAATTG
1 AAAAAAAATTG
17256302 AAAAAAAATTG
1 AAAAAAAATTG
17256313 AAAAAAAA
1 AAAAAAAA
17256321 AATTGCATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (11 bp):
AAAAAAAATTG
Found at i:17256310 original size:24 final size:24
Alignment explanation
Indices: 17256278--17256325 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
17256268 TGTAGATTCA
17256278 AAAAAAAATCGAAAAAAAAAATTG
1 AAAAAAAATCGAAAAAAAAAATTG
*
17256302 AAAAAAAATTGAAAAAAAAAATTG
1 AAAAAAAATCGAAAAAAAAAATTG
17256326 CATACGGTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.15
Consensus pattern (24 bp):
AAAAAAAATCGAAAAAAAAAATTG
Found at i:17262819 original size:30 final size:30
Alignment explanation
Indices: 17262785--17262881 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
17262775 AGCTCACTCC
17262785 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
17262815 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
17262845 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
17262875 TAGCTCA
1 TAGCTCA
17262882 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:17264618 original size:13 final size:13
Alignment explanation
Indices: 17264600--17264639 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
17264590 AAAGGAGAAG
17264600 AAATTCAGAAAAA
1 AAATTCAGAAAAA
17264613 AAATTCA-AAAAA
1 AAATTCAGAAAAA
*
17264625 AAAATC-GAAAAA
1 AAATTCAGAAAAA
17264637 AAA
1 AAA
17264640 GGAAAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 18 0.72
13 7 0.28
ACGTcount: A:0.75, C:0.07, G:0.05, T:0.12
Consensus pattern (13 bp):
AAATTCAGAAAAA
Found at i:17264625 original size:12 final size:12
Alignment explanation
Indices: 17264600--17264639 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
17264590 AAAGGAGAAG
17264600 AAATTCAGAAAAA
1 AAATTCA-AAAAA
17264613 AAATTCAAAAAA
1 AAATTCAAAAAA
*
17264625 AAAATCGAAAAAA
1 AAATTC-AAAAAA
17264638 AA
1 AA
17264640 GGAAAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.75, C:0.07, G:0.05, T:0.12
Consensus pattern (12 bp):
AAATTCAAAAAA
Found at i:17265629 original size:37 final size:37
Alignment explanation
Indices: 17265578--17265648 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
17265568 CATTCTTGTA
17265578 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
17265615 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
17265649 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:17265648 original size:6 final size:6
Alignment explanation
Indices: 17265588--17265637 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
17265578 AAGAGAAAAC
*
17265588 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
17265637 A
1 A
17265638 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:17265730 original size:11 final size:12
Alignment explanation
Indices: 17265698--17265728 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
17265688 TTGAGAGAAC
17265698 TTGAAAAAGCCT
1 TTGAAAAAGCCT
17265710 TTGAAAAAGCCT
1 TTGAAAAAGCCT
17265722 TTGAAAA
1 TTGAAAA
17265729 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:17267932 original size:30 final size:30
Alignment explanation
Indices: 17267898--17267994 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
17267888 AGCTCACTCC
17267898 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
17267928 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
17267958 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
17267988 TAGCTCA
1 TAGCTCA
17267995 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:17273334 original size:22 final size:22
Alignment explanation
Indices: 17273296--17273350 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
17273286 GAATATTTAC
*
17273296 ATAAAAATTAAACTAAGTAAAA
1 ATAAAAAATAAACTAAGTAAAA
17273318 ATAAATAAATAAA-TAAGTAAAA
1 ATAAA-AAATAAACTAAGTAAAA
17273340 AT-AAAAATAAA
1 ATAAAAAATAAA
17273351 ACTTTACAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 7 0.23
21 2 0.06
22 16 0.52
23 6 0.19
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.22
Consensus pattern (22 bp):
ATAAAAAATAAACTAAGTAAAA
Found at i:17275587 original size:56 final size:55
Alignment explanation
Indices: 17275471--17275588 Score: 150
Period size: 55 Copynumber: 2.1 Consensus size: 55
17275461 TGCATGCTTT
* * * * *
17275471 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTAATTTAATTCATGTTTTGCTGCA
*
17275525 CTTTAAATGCCGTTCCATACATGG-GAACATCTAATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTAATTTAATTCATGT-TTTGCTGCA
17275581 CATTAAAT
1 CATTAAAT
17275589 CAGCAAGCAG
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
54 3 0.06
55 27 0.50
56 24 0.44
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTAATTTAATTCATGTTTTGCTGCA
Found at i:17280094 original size:15 final size:15
Alignment explanation
Indices: 17280074--17280104 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
17280064 CCAACCTTCA
17280074 AATTTTACCTCAATT
1 AATTTTACCTCAATT
17280089 AATTTTACCTCAATT
1 AATTTTACCTCAATT
17280104 A
1 A
17280105 TACATAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTTTACCTCAATT
Found at i:17282364 original size:11 final size:11
Alignment explanation
Indices: 17282348--17282374 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
17282338 TAGAAATTAG
17282348 TTTGTGAAACT
1 TTTGTGAAACT
17282359 TTTGTGAAACT
1 TTTGTGAAACT
17282370 TTTGT
1 TTTGT
17282375 ATTGATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.07, G:0.19, T:0.52
Consensus pattern (11 bp):
TTTGTGAAACT
Found at i:17283906 original size:93 final size:92
Alignment explanation
Indices: 17283774--17283968 Score: 286
Period size: 93 Copynumber: 2.1 Consensus size: 92
17283764 TTGATTTTAG
* *
17283774 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTA-TATAATTA
1 TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTA-AATTA
* *
17283838 TATTTAAT-ATTAATTATTTTAAATTGTA
65 TATGTAATAATT-ATTATTTTAAATTATA
* *
17283866 TAAATTCATATAAGAAAATTTTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTA
1 TAAATTCATATAAGAAAA-TTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTA
17283931 TATGTAATAATTATTATTTTAAATTATA
65 TATGTAATAATTATTATTTTAAATTATA
*
17283959 CAAATTCATA
1 TAAATTCATA
17283969 AACTATAATC
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
92 17 0.18
93 71 0.76
94 5 0.05
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (92 bp):
TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTAT
ATGTAATAATTATTATTTTAAATTATA
Found at i:17284026 original size:17 final size:17
Alignment explanation
Indices: 17284001--17284034 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
17283991 ATAATTTTAA
*
17284001 ATTTTATTAAATCATAT
1 ATTTAATTAAATCATAT
17284018 ATTTAATTAAATCATAT
1 ATTTAATTAAATCATAT
17284035 TTAATATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAATTAAATCATAT
Found at i:17284036 original size:15 final size:16
Alignment explanation
Indices: 17284001--17284039 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
17283991 ATAATTTTAA
*
17284001 ATTTTATTAAATCATAT
1 ATTTAATTAAATCA-AT
17284018 ATTTAATTAAATC-AT
1 ATTTAATTAAATCAAT
17284033 ATTTAAT
1 ATTTAAT
17284040 ATTAATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.43
17 12 0.57
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTTAATTAAATCAAT
Found at i:17284043 original size:17 final size:18
Alignment explanation
Indices: 17284005--17284044 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
17283995 TTTTAAATTT
*
17284005 TATTAAATCATATATTTA
1 TATTAAATCATATATTAA
17284023 -ATTAAATCATAT-TTAA
1 TATTAAATCATATATTAA
17284039 TATTAA
1 TATTAA
17284045 TTATTTGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTAAATCATATATTAA
Found at i:17284159 original size:15 final size:15
Alignment explanation
Indices: 17284124--17284258 Score: 70
Period size: 15 Copynumber: 8.9 Consensus size: 15
17284114 TTAAGAATTT
*
17284124 TATTAAATTAT-ATA
1 TATTTAATTATAATA
17284138 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
17284152 TATTTAATAATAAT-
1 TATTTAATTATAATA
17284166 TATGTTAATT-T-ATA
1 TAT-TTAATTATAATA
* *
17284180 T-TTTACAGTATCATA
1 TATTTA-ATTATAATA
*
17284195 TATTATGATTTGAGTAAATTCA
1 TATT-T-AATT-A-T-AA-T-A
*
17284217 TATTAAATTAT-ATA
1 TATTTAATTATAATA
17284231 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
17284245 TATTTAATAATAAT
1 TATTTAATTATAAT
17284259 TATGTTTAAA
Statistics
Matches: 93, Mismatches: 11, Indels: 33
0.68 0.08 0.24
Matches are distributed among these distances:
12 3 0.03
13 21 0.23
14 17 0.18
15 32 0.34
16 3 0.03
17 2 0.02
18 3 0.03
19 2 0.02
20 4 0.04
21 1 0.01
22 5 0.05
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:17284166 original size:120 final size:119
Alignment explanation
Indices: 17284000--17284218 Score: 345
Period size: 120 Copynumber: 1.8 Consensus size: 119
17283990 AATAATTTTA
* *
17284000 AATTTTATTAAATCATATATTTAATTAAATCATATTTAATATTAATTAT-TTGAAATTT-TCTTT
1 AATTTTATTAAATCATATATTTAATTAAATCATATTTAATAATAATTATGTT--AATTTATATTT
*
17284063 TATAGTATCATATATTATGATTTGAGTAAATTCATAGAAGAATTTTATTTATTAAG
64 TACAGTATCATATATTATGATTTGAGTAAATTCATAGAAGAATTTTATTTATTAAG
*
17284119 AATTTTATTAAATTATATATTTTAATTATAAT-ATATTTAATAATAATTATGTTAATTTATATTT
1 AATTTTATTAAATCATATA-TTTAATTA-AATCATATTTAATAATAATTATGTTAATTTATATTT
17284183 TACAGTATCATATATTATGATTTGAGTAAATTCATA
64 TACAGTATCATATATTATGATTTGAGTAAATTCATA
17284219 TTAAATTATA
Statistics
Matches: 92, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
119 23 0.25
120 64 0.70
121 5 0.05
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (119 bp):
AATTTTATTAAATCATATATTTAATTAAATCATATTTAATAATAATTATGTTAATTTATATTTTA
CAGTATCATATATTATGATTTGAGTAAATTCATAGAAGAATTTTATTTATTAAG
Found at i:17284247 original size:16 final size:16
Alignment explanation
Indices: 17284226--17284267 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
17284216 ATATTAAATT
*
17284226 ATATATTTTAATTATA
1 ATATATTTTAATAATA
17284242 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
17284257 AT-TATGTTTAA
1 ATATAT-TTTAA
17284268 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:17284375 original size:154 final size:156
Alignment explanation
Indices: 17284217--17284514 Score: 539
Period size: 154 Copynumber: 1.9 Consensus size: 156
17284207 AGTAAATTCA
17284217 TATTAAATTATATATTTTAATTATAA-TATATTTAATAATAATTATGTTTAAATATGATTAAATT
1 TATTAAATTATATATTTTAATTA-AATTATATTTAATAATAATTATGTTTAAATATGATTAAATT
17284281 ATTTATTATTGAT-AT-TAATCTTATTAAAATTTAAATAACAATAACAATAATAATTTACCAAAA
65 ATTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAACAATAATAATTTACCAAAA
17284344 CAAATTTATGCTAATTATTAAGAATTT
130 CAAATTTATGCTAATTATTAAGAATTT
17284371 TATTAAATTATATATTTTAATTAAATTATATTTAATAATAATTATGTTTAAATATGATTAAATTA
1 TATTAAATTATATATTTTAATTAAATTATATTTAATAATAATTATGTTTAAATATGATTAAATTA
*
17284436 TTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATAATCATTTACCAAAA
66 TTTATTATTGATAAT-ATAATCTTATTAAAATTTAAATAACAATAACAATAATAATTTACCAAAA
*
17284501 CAAATTTCTGCTAA
130 CAAATTTATGCTAA
17284515 GGGTATTCTA
Statistics
Matches: 138, Mismatches: 2, Indels: 5
0.95 0.01 0.03
Matches are distributed among these distances:
153 2 0.01
154 74 0.54
155 2 0.01
157 60 0.43
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (156 bp):
TATTAAATTATATATTTTAATTAAATTATATTTAATAATAATTATGTTTAAATATGATTAAATTA
TTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAACAATAATAATTTACCAAAAC
AAATTTATGCTAATTATTAAGAATTT
Found at i:17284395 original size:18 final size:17
Alignment explanation
Indices: 17284367--17284401 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
17284357 ATTATTAAGA
17284367 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
17284384 ATTTTAATTAAATTATAT
1 ATTTT-ATTAAATTATAT
17284402 TTAATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:17284655 original size:16 final size:16
Alignment explanation
Indices: 17284634--17284672 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
17284624 TTGATTTGCT
*
17284634 ATTACACAGCTTTTCC
1 ATTACACAGCTATTCC
**
17284650 ATTACACCTCTATTCC
1 ATTACACAGCTATTCC
17284666 ATTACAC
1 ATTACAC
17284673 CTCTAATCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.33, G:0.03, T:0.36
Consensus pattern (16 bp):
ATTACACAGCTATTCC
Found at i:17284673 original size:16 final size:16
Alignment explanation
Indices: 17284647--17284703 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
17284637 ACACAGCTTT
* *
17284647 TCCATTACACCTCTAT
1 TCCAATACACCTCTAA
*
17284663 TCCATTACACCTCTAA
1 TCCAATACACCTCTAA
17284679 TCCAATACACCTCTAA
1 TCCAATACACCTCTAA
17284695 TCCAATACA
1 TCCAATACA
17284704 GCGAACCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (16 bp):
TCCAATACACCTCTAA
Found at i:17284849 original size:20 final size:20
Alignment explanation
Indices: 17284824--17284878 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
17284814 ACGAGTTAAA
* *
17284824 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
17284844 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
*
17284864 TTGAGCTCAAATGAG
1 TTGAGCTCGAATGAG
17284879 TTGAACCACA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:17287049 original size:18 final size:19
Alignment explanation
Indices: 17287004--17287052 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
17286994 GAATATTTAC
*
17287004 ATAAAAATTAAACTAAGTAA
1 ATAAAAA-TAAACTAAATAA
17287024 A-AATAAATAAA-TAAATAA
1 ATAA-AAATAAACTAAATAA
17287042 ATAAAAATAAA
1 ATAAAAATAAA
17287053 AATAAAACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 14 0.54
19 8 0.31
20 4 0.15
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (19 bp):
ATAAAAATAAACTAAATAA
Found at i:17295342 original size:23 final size:23
Alignment explanation
Indices: 17295312--17295377 Score: 114
Period size: 23 Copynumber: 2.9 Consensus size: 23
17295302 CTTTTTGAAC
*
17295312 CATTTCCATTTCGAACCAAATTA
1 CATTTCCATTTCGTACCAAATTA
17295335 CATTTCCATTTCGTACCAAATTA
1 CATTTCCATTTCGTACCAAATTA
*
17295358 CATTACCATTTCGTACCAAA
1 CATTTCCATTTCGTACCAAA
17295378 CCCAAACCAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (23 bp):
CATTTCCATTTCGTACCAAATTA
Found at i:17295759 original size:21 final size:22
Alignment explanation
Indices: 17295734--17295792 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 22
17295724 AATATTCATA
17295734 CGAAATTAAAAAAAAGTGAATT
1 CGAAATTAAAAAAAAGTGAATT
**
17295756 -GAAATTTTAAAAAA---AATT
1 CGAAATTAAAAAAAAGTGAATT
17295774 CGAGAATTAAAAAAAAGTG
1 CGA-AATTAAAAAAAAGTG
17295793 TTTCGCGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 9
0.68 0.10 0.22
Matches are distributed among these distances:
18 4 0.14
19 2 0.07
20 10 0.36
21 12 0.43
ACGTcount: A:0.59, C:0.03, G:0.14, T:0.24
Consensus pattern (22 bp):
CGAAATTAAAAAAAAGTGAATT
Found at i:17300571 original size:23 final size:22
Alignment explanation
Indices: 17300520--17300571 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
17300510 CCTCGTCTTT
*
17300520 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
17300542 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
17300565 TTCTTTT
1 TTCTTTT
17300572 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:17307895 original size:23 final size:22
Alignment explanation
Indices: 17307843--17307895 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
17307833 TCCACGTCTT
*
17307843 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
17307865 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
17307888 TTTCTTTT
1 TTTCTTTT
17307896 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:17316615 original size:6 final size:6
Alignment explanation
Indices: 17316604--17316629 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
17316594 AGTTGTAAAG
17316604 TTTTAT TTTTAT TTTTAT TTTTAT TT
1 TTTTAT TTTTAT TTTTAT TTTTAT TT
17316630 ATTTATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:17316632 original size:4 final size:4
Alignment explanation
Indices: 17316623--17316650 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
17316613 TATTTTTATT
17316623 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
17316651 CTTAGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:17317565 original size:11 final size:10
Alignment explanation
Indices: 17317529--17317564 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
17317519 ACGGTATTGT
*
17317529 AAAAAAAAT-
1 AAAAAAATTC
17317538 AAAAAAATTC
1 AAAAAAATTC
17317548 AAAAAAATTC
1 AAAAAAATTC
17317558 AAAAAAA
1 AAAAAAA
17317565 AGTTTGTGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 8 0.32
10 17 0.68
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.14
Consensus pattern (10 bp):
AAAAAAATTC
Found at i:17320635 original size:20 final size:20
Alignment explanation
Indices: 17320596--17320636 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
17320586 AAAAATGAAA
*
17320596 AATTTTTTTTGTTGTAATTT
1 AATTTTTTTTCTTGTAATTT
17320616 AATTTTTTTTCCTTGT-ATTT
1 AATTTTTTTT-CTTGTAATTT
17320636 A
1 A
17320637 GCTTACTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.20, C:0.05, G:0.07, T:0.68
Consensus pattern (20 bp):
AATTTTTTTTCTTGTAATTT
Found at i:17320669 original size:17 final size:16
Alignment explanation
Indices: 17320658--17320695 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 16
17320648 TATTGGAGTA
17320658 TCAAAAAAATTGAAAT
1 TCAAAAAAATTGAAAT
17320674 TCAAAAAAA---AAAT
1 TCAAAAAAATTGAAAT
17320687 TCAAAAAAA
1 TCAAAAAAA
17320696 AGTGAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 13 0.59
16 9 0.41
ACGTcount: A:0.71, C:0.08, G:0.03, T:0.18
Consensus pattern (16 bp):
TCAAAAAAATTGAAAT
Found at i:17320718 original size:26 final size:25
Alignment explanation
Indices: 17320689--17320759 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 25
17320679 AAAAAAATTC
17320689 AAAAAAAAGTGAAAAAAATCGAGCAA
1 AAAAAAAAGTGAAAAAAAT-GAGCAA
** *
17320715 AAAAAAAGAAAGAAAAAAGTGAGCAA
1 AAAAAAA-AGTGAAAAAAATGAGCAA
* *
17320741 AAAAATCAAGTTAAAAAAA
1 AAAAA-AAAGTGAAAAAAA
17320760 AAAGAGAAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
26 25 0.71
27 10 0.29
ACGTcount: A:0.72, C:0.06, G:0.14, T:0.08
Consensus pattern (25 bp):
AAAAAAAAGTGAAAAAAATGAGCAA
Found at i:17321781 original size:12 final size:12
Alignment explanation
Indices: 17321760--17321913 Score: 69
Period size: 12 Copynumber: 13.6 Consensus size: 12
17321750 AGAAAAGGAG
*
17321760 AAAGAGATTGAA
1 AAAGAAATTGAA
17321772 AAAGAAATTG--
1 AAAGAAATTGAA
**
17321782 AAAGAAA-ACAA
1 AAAGAAATTGAA
*
17321793 AAAGAAAATGAA
1 AAAGAAATTGAA
**
17321805 AAAGAAAAAGAA
1 AAAGAAATTGAA
** *
17321817 ATTGCAAA-AGAA
1 AAAG-AAATTGAA
*
17321829 AAAGAAATCGAA
1 AAAGAAATTGAA
** **
17321841 AAAGTGAGAGAA
1 AAAGAAATTGAA
*
17321853 AAAGAAAATG-A
1 AAAGAAATTGAA
17321864 AAAGAAAATTGAA
1 AAAG-AAATTGAA
17321877 AAAGAAATTG--
1 AAAGAAATTGAA
17321887 --AG-AA-TGAA
1 AAAGAAATTGAA
*
17321895 AAAAAAATTGAA
1 AAAGAAATTGAA
17321907 AAAGAAA
1 AAAGAAA
17321914 AAGCGAAAAA
Statistics
Matches: 107, Mismatches: 22, Indels: 26
0.69 0.14 0.17
Matches are distributed among these distances:
6 2 0.02
7 2 0.02
8 2 0.02
10 8 0.07
11 17 0.16
12 68 0.64
13 8 0.07
ACGTcount: A:0.69, C:0.02, G:0.18, T:0.11
Consensus pattern (12 bp):
AAAGAAATTGAA
Found at i:17321805 original size:6 final size:6
Alignment explanation
Indices: 17321782--17321916 Score: 78
Period size: 6 Copynumber: 22.7 Consensus size: 6
17321772 AAAGAAATTG
* * ** *
17321782 AAAG-A AAACAA AAAGAA AATGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
17321829 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATG-A AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AA-AGAA
** * * *
17321877 AAAGAA ATTGAG AATGAA AAA-AA AATTGAA AAAGAA AAAG
1 AAAGAA AAAGAA AAAGAA AAAGAA AA-AGAA AAAGAA AAAG
17321917 CGAAAAAAGA
Statistics
Matches: 93, Mismatches: 32, Indels: 9
0.69 0.24 0.07
Matches are distributed among these distances:
5 11 0.12
6 73 0.78
7 9 0.10
ACGTcount: A:0.70, C:0.02, G:0.18, T:0.10
Consensus pattern (6 bp):
AAAGAA
Found at i:17321812 original size:18 final size:18
Alignment explanation
Indices: 17321786--17321916 Score: 97
Period size: 18 Copynumber: 7.3 Consensus size: 18
17321776 AAATTGAAAG
*
17321786 AAAACAAAAAGAAAATGA
1 AAAAGAAAAAGAAAATGA
* *
17321804 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAATGA
17321822 AAAAGAAAAAG-AAATCGA
1 AAAAGAAAAAGAAAAT-GA
** * *
17321840 AAAAGTGAGAGAAAAAGA
1 AAAAGAAAAAGAAAATGA
*
17321858 AAATG-AAAAGAAAATTGA
1 AAAAGAAAAAGAAAA-TGA
** *
17321876 AAAAGAAATTGAGAATGA
1 AAAAGAAAAAGAAAATGA
* *
17321894 AAAA-AAAATTGAAAAAGA
1 AAAAGAAAA-AGAAAATGA
17321912 AAAAG
1 AAAAG
17321917 CGAAAAAAGA
Statistics
Matches: 87, Mismatches: 20, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
17 13 0.15
18 65 0.75
19 9 0.10
ACGTcount: A:0.70, C:0.02, G:0.18, T:0.10
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:17321883 original size:30 final size:29
Alignment explanation
Indices: 17321769--17321916 Score: 105
Period size: 30 Copynumber: 5.2 Consensus size: 29
17321759 GAAAGAGATT
* * *
17321769 GAAAAAGAAATTGAAAGAAAA--CAAAAA
1 GAAAAAGAAAATGAAAAAAAATTGAAAAA
* * *
17321796 GAAAATGAAAAAGAAAAAGAAATTGCAAAA
1 GAAAAAGAAAATGAAAAA-AAATTGAAAAA
* *
17321826 GAAAAAG-AAATCG---AAAAAGTG--AGA
1 GAAAAAGAAAAT-GAAAAAAAATTGAAAAA
17321850 GAAAAAGAAAATGAAAAGAAAATTGAAAAA
1 GAAAAAGAAAATGAAAA-AAAATTGAAAAA
** *
17321880 GAAATTGAGAATGAAAAAAAAATTGAAAAA
1 GAAAAAGAAAATG-AAAAAAAATTGAAAAA
17321910 GAAAAAG
1 GAAAAAG
17321917 CGAAAAAAGA
Statistics
Matches: 92, Mismatches: 17, Indels: 21
0.71 0.13 0.16
Matches are distributed among these distances:
24 10 0.11
25 4 0.04
26 5 0.05
27 17 0.18
28 9 0.10
29 3 0.03
30 40 0.43
31 4 0.04
ACGTcount: A:0.70, C:0.02, G:0.18, T:0.10
Consensus pattern (29 bp):
GAAAAAGAAAATGAAAAAAAATTGAAAAA
Found at i:17328835 original size:13 final size:12
Alignment explanation
Indices: 17328777--17328832 Score: 87
Period size: 12 Copynumber: 4.7 Consensus size: 12
17328767 TAGTTTCTTC
17328777 AAAAAAAATTCG-
1 AAAAAAAATT-GA
*
17328789 AAAAAAAATTCA
1 AAAAAAAATTGA
17328801 AAAAAAAATTGA
1 AAAAAAAATTGA
17328813 AAAAAAAATTGA
1 AAAAAAAATTGA
17328825 AAAAAAAA
1 AAAAAAAA
17328833 ATTTGGTTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
12 41 1.00
ACGTcount: A:0.77, C:0.04, G:0.05, T:0.14
Consensus pattern (12 bp):
AAAAAAAATTGA
Found at i:17328892 original size:15 final size:16
Alignment explanation
Indices: 17328872--17328912 Score: 66
Period size: 17 Copynumber: 2.6 Consensus size: 16
17328862 GATATCAAGT
17328872 TGAAAAAAAAA-TTCG
1 TGAAAAAAAAATTTCG
17328887 TGAAAAAAAAATTTTCG
1 TGAAAAAAAAA-TTTCG
17328904 TGAAAAAAA
1 TGAAAAAAA
17328913 GAAGAAGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 11 0.46
17 13 0.54
ACGTcount: A:0.61, C:0.05, G:0.12, T:0.22
Consensus pattern (16 bp):
TGAAAAAAAAATTTCG
Found at i:17337956 original size:15 final size:16
Alignment explanation
Indices: 17337936--17337967 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
17337926 AGAAAATGAA
17337936 AAAGAAAAAGAA-ATG
1 AAAGAAAAAGAAGATG
17337951 AAAGAAAAAGAAGATG
1 AAAGAAAAAGAAGATG
17337967 A
1 A
17337968 GTGTGAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAGAAGATG
Found at i:17338100 original size:21 final size:18
Alignment explanation
Indices: 17338076--17338120 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 18
17338066 ACGAGAGTAC
17338076 AAAAGAAATGAGTGATGTGA
1 AAAAGAAA-GAG-GATGTGA
*
17338096 TAAAAGAAAGAGGATTTGA
1 -AAAAGAAAGAGGATGTGA
17338115 AAAAGA
1 AAAAGA
17338121 GTTTGAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 6 0.26
19 6 0.26
20 3 0.13
21 8 0.35
ACGTcount: A:0.56, C:0.00, G:0.27, T:0.18
Consensus pattern (18 bp):
AAAAGAAAGAGGATGTGA
Found at i:17340989 original size:30 final size:30
Alignment explanation
Indices: 17340955--17341051 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
17340945 AGCTCACTCC
17340955 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
17340985 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
17341015 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
17341045 TAGCTCA
1 TAGCTCA
17341052 TTTTAGTTTT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:17342785 original size:20 final size:20
Alignment explanation
Indices: 17342748--17342804 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
17342738 TTGGATTTAA
* *
17342748 AAAAAAAAGAGAAGAAATTC-
1 AAAAAAAAGA-AAAAAAATCG
*
17342768 AAAAAAAATAAAAAAAATCG
1 AAAAAAAAGAAAAAAAATCG
*
17342788 AAAAAAAGGAAAAAAAA
1 AAAAAAAAGAAAAAAAA
17342805 GTGAAAATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 7 0.23
20 24 0.77
ACGTcount: A:0.79, C:0.04, G:0.11, T:0.07
Consensus pattern (20 bp):
AAAAAAAAGAAAAAAAATCG
Found at i:17343756 original size:16 final size:16
Alignment explanation
Indices: 17343737--17343777 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
17343727 AAGAGAAAAC
17343737 AAAGAAAAGAAAAGAA
1 AAAGAAAAGAAAAGAA
*
17343753 AAAGAAAATG-AAATAA
1 AAAGAAAA-GAAAAGAA
17343769 AAA-AAAAGA
1 AAAGAAAAGA
17343778 GAGGCAAGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
14 1 0.05
15 4 0.18
16 16 0.73
17 1 0.05
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (16 bp):
AAAGAAAAGAAAAGAA
Found at i:17343857 original size:11 final size:12
Alignment explanation
Indices: 17343825--17343855 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
17343815 TTGAGAGAAC
17343825 TTGAAAAAGCCT
1 TTGAAAAAGCCT
17343837 TTGAAAAAGCCT
1 TTGAAAAAGCCT
17343849 TTGAAAA
1 TTGAAAA
17343856 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:17346070 original size:30 final size:30
Alignment explanation
Indices: 17346036--17346132 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
17346026 AGCTCACTCC
17346036 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
17346066 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
17346096 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
17346126 TAGCTCA
1 TAGCTCA
17346133 TTTTAGTTTT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:17360142 original size:20 final size:20
Alignment explanation
Indices: 17360096--17360142 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
17360086 AGCTTGTTTC
*
17360096 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
17360116 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
17360136 CAGCTCA
1 CAGCTCA
17360143 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:17361995 original size:10 final size:10
Alignment explanation
Indices: 17361971--17362019 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
17361961 AGCTCGTTTC
*
17361971 CAGCTCACTT
1 CAGCTCAATT
* *
17361981 GAGCTCAAGT
1 CAGCTCAATT
17361991 CAGCTC-ATT
1 CAGCTCAATT
17362000 CGAGCTCAATT
1 C-AGCTCAATT
17362011 CAGCTCAAT
1 CAGCTCAAT
17362020 CTTAACCCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 3 0.09
10 25 0.78
11 4 0.12
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.27
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:17361996 original size:20 final size:20
Alignment explanation
Indices: 17361971--17362017 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
17361961 AGCTCGTTTC
17361971 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGCTCAAGT
*
17361991 CAGCTCATTCGAGCTCAATT
1 CAGCTCATTCGAGCTCAAGT
17362011 CAGCTCA
1 CAGCTCA
17362018 ATCTTAACCC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGCTCAAGT
Found at i:17366033 original size:10 final size:10
Alignment explanation
Indices: 17366018--17366066 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
17366008 TTGGGTTAAG
17366018 ATTGAGCTGA
1 ATTGAGCTGA
*
17366028 ATTGAGCTCA
1 ATTGAGCTGA
*
17366038 AATGAGCTGA
1 ATTGAGCTGA
* *
17366048 CTTGAGCTCA
1 ATTGAGCTGA
*
17366058 AGTGAGCTG
1 ATTGAGCTG
17366067 GAAACGAGCT
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.27
Consensus pattern (10 bp):
ATTGAGCTGA
Found at i:17366043 original size:20 final size:20
Alignment explanation
Indices: 17366020--17366066 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
17366010 GGGTTAAGAT
17366020 TGAGCTGAATTGAGCTCAAA
1 TGAGCTGAATTGAGCTCAAA
* *
17366040 TGAGCTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAA
17366060 TGAGCTG
1 TGAGCTG
17366067 GAAACGAGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAA
Found at i:17370911 original size:30 final size:30
Alignment explanation
Indices: 17370877--17370973 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
17370867 TAAACTAAAA
*
17370877 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
17370907 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
17370937 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
17370966 ATGAGCTA
1 -TGAGCTA
17370974 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:17373167 original size:12 final size:12
Alignment explanation
Indices: 17373152--17373182 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
17373142 TTCTTTTTGC
17373152 TTTTCAAAGGCT
1 TTTTCAAAGGCT
17373164 TTTTCAAAGGCT
1 TTTTCAAAGGCT
17373176 TTTTCAA
1 TTTTCAA
17373183 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:17373259 original size:6 final size:6
Alignment explanation
Indices: 17373243--17373292 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
17373233 TTTCTTTTTA
*
17373243 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
17373292 T
1 T
17373293 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:17373275 original size:37 final size:37
Alignment explanation
Indices: 17373232--17373302 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
17373222 CTTGCCTCTC
17373232 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
17373269 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
17373303 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Done.