Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 53 of 203
Found at i:17392152 original size:26 final size:26
Alignment explanation
Indices: 17392101--17392154 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
17392091 AATTTTAATT
* *
17392101 TTTTTAAAATATTTTTTTATTTTTTA
1 TTTTTAAAATATTTTTTTAGTGTTTA
*
17392127 TTTTTAAAATATTTTTTTGGTGTTTA
1 TTTTTAAAATATTTTTTTAGTGTTTA
17392153 TT
1 TT
17392155 AAAAAATTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (26 bp):
TTTTTAAAATATTTTTTTAGTGTTTA
Found at i:17392653 original size:21 final size:21
Alignment explanation
Indices: 17392627--17392671 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
17392617 TTAAAATAAA
17392627 TTTTTTTATAATTGATAAAGT
1 TTTTTTTATAATTGATAAAGT
17392648 TTTTTTTATAATTGATAAAGT
1 TTTTTTTATAATTGATAAAGT
17392669 TTT
1 TTT
17392672 AAATTAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.60
Consensus pattern (21 bp):
TTTTTTTATAATTGATAAAGT
Found at i:17392679 original size:20 final size:21
Alignment explanation
Indices: 17392633--17392679 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
17392623 TAAATTTTTT
***
17392633 TATAATTGATAAAGTTTTTTT
1 TATAATTGATAAAGTTTTAAA
17392654 TATAATTGATAAAGTTTTAAA
1 TATAATTGATAAAGTTTTAAA
17392675 T-TAAT
1 TATAAT
17392680 AATAGTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (21 bp):
TATAATTGATAAAGTTTTAAA
Found at i:17394015 original size:27 final size:27
Alignment explanation
Indices: 17393981--17394039 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
17393971 AAAAAATAAT
*
17393981 CAAAATATTATAACTTTTTTTATTTAC
1 CAAAATATTATAACTTTTTTTATTTAA
*
17394008 CAAAATATTATAATTTTTTTTATTTAA
1 CAAAATATTATAACTTTTTTTATTTAA
17394035 CAAAA
1 CAAAA
17394040 AACAAAAACT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.49
Consensus pattern (27 bp):
CAAAATATTATAACTTTTTTTATTTAA
Found at i:17394703 original size:15 final size:15
Alignment explanation
Indices: 17394683--17394732 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
17394673 ATTACCAAAA
17394683 TAGAGTTTATTAAAT
1 TAGAGTTTATTAAAT
*
17394698 TAGAGTTTATTAGAT
1 TAGAGTTTATTAAAT
*
17394713 GAGAATAGTTTATTAAAT
1 TAG---AGTTTATTAAAT
17394731 TA
1 TA
17394733 AAATAGAGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
15 16 0.57
18 12 0.43
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (15 bp):
TAGAGTTTATTAAAT
Found at i:17394798 original size:91 final size:91
Alignment explanation
Indices: 17394695--17395073 Score: 758
Period size: 91 Copynumber: 4.2 Consensus size: 91
17394685 GAGTTTATTA
17394695 AATTAGAGTTTATTAGATGAGAATAGTTTATTAAATTAAAATAGAGTTATTACTTAATTAGAATT
1 AATTAGAGTTTATTAGATGAGAATAGTTTATTAAATTAAAATAGAGTTATTACTTAATTAGAATT
17394760 CTAAGCATCTTAATTATCACTTAACT
66 CTAAGCATCTTAATTATCACTTAACT
17394786 AATTAGAGTTTATTAGATGAGAATAGTTTATTAAATTAAAATAGAGTTATTACTTAATTAGAATT
1 AATTAGAGTTTATTAGATGAGAATAGTTTATTAAATTAAAATAGAGTTATTACTTAATTAGAATT
17394851 CTAAGCATCTTAATTATCACTTAACT
66 CTAAGCATCTTAATTATCACTTAACT
17394877 AATTAGAGTTTATTAGATGAGAATAGTTTATTAAATTAAAATAGAGTTATTACTTAATTAGAATT
1 AATTAGAGTTTATTAGATGAGAATAGTTTATTAAATTAAAATAGAGTTATTACTTAATTAGAATT
17394942 CTAAGCATCTTAATTATCACTTAACT
66 CTAAGCATCTTAATTATCACTTAACT
17394968 AATTAGAGTTTATTAGATGAGAATAGTTTATTAAATTAAAATAGAGTTATTACTTAATTAGAATT
1 AATTAGAGTTTATTAGATGAGAATAGTTTATTAAATTAAAATAGAGTTATTACTTAATTAGAATT
17395033 CTAAGCATCTTAATTATCACTTAACT
66 CTAAGCATCTTAATTATCACTTAACT
17395059 AATTAGAGTTTATTA
1 AATTAGAGTTTATTA
17395074 CTTAATTCAC
Statistics
Matches: 288, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 288 1.00
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (91 bp):
AATTAGAGTTTATTAGATGAGAATAGTTTATTAAATTAAAATAGAGTTATTACTTAATTAGAATT
CTAAGCATCTTAATTATCACTTAACT
Found at i:17395284 original size:27 final size:28
Alignment explanation
Indices: 17395231--17395295 Score: 105
Period size: 28 Copynumber: 2.4 Consensus size: 28
17395221 TTTTTTTTGT
* *
17395231 ATATTTTGGTAAATAAAAAAACTTTATA
1 ATATTTTGATAAATAAAAAAACGTTATA
17395259 ATATTTTGATAAATAAAAAAA-GTTATA
1 ATATTTTGATAAATAAAAAAACGTTATA
17395286 ATATTTTGAT
1 ATATTTTGAT
17395296 TATTTTTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 15 0.43
28 20 0.57
ACGTcount: A:0.49, C:0.02, G:0.08, T:0.42
Consensus pattern (28 bp):
ATATTTTGATAAATAAAAAAACGTTATA
Found at i:17406438 original size:5 final size:5
Alignment explanation
Indices: 17406428--17406468 Score: 55
Period size: 5 Copynumber: 8.0 Consensus size: 5
17406418 ACAGAAATGA
* *
17406428 GTTTT GTTTT GTTTT GTTTT GTTTT GTCTG GTTTTT GTTTT
1 GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT G-TTTT GTTTT
17406469 AATTGATGTC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
5 28 0.90
6 3 0.10
ACGTcount: A:0.00, C:0.02, G:0.22, T:0.76
Consensus pattern (5 bp):
GTTTT
Found at i:17407488 original size:2 final size:2
Alignment explanation
Indices: 17407483--17407512 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
17407473 ATATTATATA
17407483 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
17407513 GTTGTTGCCT
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:17411331 original size:18 final size:18
Alignment explanation
Indices: 17411317--17411351 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
17411307 GTAATTAATT
17411317 TAAAATT-TTTAATTAAA
1 TAAAATTATTTAATTAAA
17411334 TAAAATTATTTAATTAAA
1 TAAAATTATTTAATTAAA
17411352 AATCTATTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TAAAATTATTTAATTAAA
Found at i:17412152 original size:256 final size:256
Alignment explanation
Indices: 17411697--17412209 Score: 1017
Period size: 256 Copynumber: 2.0 Consensus size: 256
17411687 AAAATAAAAC
17411697 ATTAAAAAATAAAAAAATTAGCACCATGCGATTATAATATTTAAAAATTTTAATTTTTAATTCAT
1 ATTAAAAAATAAAAAAATTAGCACCATGCGATTATAATATTTAAAAATTTTAATTTTTAATTCAT
17411762 ATTTCCATTAGGAAACATTAAAATCATTTTTTTAACGTTGATCAAATTCGAACTTTTTAAAGTTT
66 ATTTCCATTAGGAAACATTAAAATCATTTTTTTAACGTTGATCAAATTCGAACTTTTTAAAGTTT
17411827 TAGAACTAAATTTAATTAAAAATAATATAAAAATATAAAAATTAAAAGTTTAATTTATCTGTAGT
131 TAGAACTAAATTTAATTAAAAATAATATAAAAATATAAAAATTAAAAGTTTAATTTATCTGTAGT
*
17411892 ATTAATTTTCAATTATAATAAATTTGCCTATATTTTTATCATTAAACGAAGTTAACCGGAT
196 ATTAATTTTCAATTATAATAAATTTGCCTATATTTTTATCATTAAACGAAGTTAAACGGAT
17411953 ATTAAAAAATAAAAAAATTAGCACCATGCGATTATAATATTTAAAAATTTTAATTTTTAATTCAT
1 ATTAAAAAATAAAAAAATTAGCACCATGCGATTATAATATTTAAAAATTTTAATTTTTAATTCAT
17412018 ATTTCCATTAGGAAACATTAAAATCATTTTTTTAACGTTGATCAAATTCGAACTTTTTAAAGTTT
66 ATTTCCATTAGGAAACATTAAAATCATTTTTTTAACGTTGATCAAATTCGAACTTTTTAAAGTTT
17412083 TAGAACTAAATTTAATTAAAAATAATATAAAAATATAAAAATTAAAAGTTTAATTTATCTGTAGT
131 TAGAACTAAATTTAATTAAAAATAATATAAAAATATAAAAATTAAAAGTTTAATTTATCTGTAGT
17412148 ATTAATTTTCAATTATAATAAATTTGCCTATATTTTTATCATTAAACGAAGTTAAACGGAT
196 ATTAATTTTCAATTATAATAAATTTGCCTATATTTTTATCATTAAACGAAGTTAAACGGAT
17412209 A
1 A
17412210 AGGCCGAAGT
Statistics
Matches: 256, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
256 256 1.00
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.40
Consensus pattern (256 bp):
ATTAAAAAATAAAAAAATTAGCACCATGCGATTATAATATTTAAAAATTTTAATTTTTAATTCAT
ATTTCCATTAGGAAACATTAAAATCATTTTTTTAACGTTGATCAAATTCGAACTTTTTAAAGTTT
TAGAACTAAATTTAATTAAAAATAATATAAAAATATAAAAATTAAAAGTTTAATTTATCTGTAGT
ATTAATTTTCAATTATAATAAATTTGCCTATATTTTTATCATTAAACGAAGTTAAACGGAT
Found at i:17412321 original size:14 final size:14
Alignment explanation
Indices: 17412280--17412329 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
17412270 AAATTTTCTT
* *
17412280 TAAAATATTAAAAA
1 TAAAAAATTAATAA
*
17412294 TAAAAAATT-GTAA
1 TAAAAAATTAATAA
17412307 TAAAAAATTAATAA
1 TAAAAAATTAATAA
17412321 TAAGAAAAT
1 TAA-AAAAT
17412330 AGTACGGGCT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 11 0.37
14 14 0.47
15 5 0.17
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (14 bp):
TAAAAAATTAATAA
Found at i:17412462 original size:83 final size:83
Alignment explanation
Indices: 17412318--17412483 Score: 314
Period size: 83 Copynumber: 2.0 Consensus size: 83
17412308 AAAAAATTAA
17412318 TAATAAGAAAATAGTACGGGCTTAATATAATATTTGGTACCTAAACTTGACAATTTCTTCTAATT
1 TAATAAGAAAATAGTACGGGCTTAATATAATATTTGGTACCTAAACTTGACAATTTCTTCTAATT
17412383 TGGAATCTAAACTTTTTT
66 TGGAATCTAAACTTTTTT
*
17412401 TAATAAGAAAATAGTACGGGCTTAATATAATATTTGGTACCTAAACTTGACAATTTTTTCTAATT
1 TAATAAGAAAATAGTACGGGCTTAATATAATATTTGGTACCTAAACTTGACAATTTCTTCTAATT
*
17412466 TGGTATCTAAACTTTTTT
66 TGGAATCTAAACTTTTTT
17412484 GGTCCAATTA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 81 1.00
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.41
Consensus pattern (83 bp):
TAATAAGAAAATAGTACGGGCTTAATATAATATTTGGTACCTAAACTTGACAATTTCTTCTAATT
TGGAATCTAAACTTTTTT
Found at i:17412470 original size:31 final size:30
Alignment explanation
Indices: 17412432--17412568 Score: 111
Period size: 31 Copynumber: 4.6 Consensus size: 30
17412422 TTAATATAAT
17412432 ATTTGGTACCTAAACTTGACAATTTTTTCTA
1 ATTTGGTACCTAAACTTGAC-ATTTTTTCTA
* * *
17412463 ATTTGGTATCTAAACTT----TTTTGGTCCA
1 ATTTGGTACCTAAACTTGACATTTT-TTCTA
* * * *
17412490 ATTAGATACCCAAACTTGACACTTTTTCCTA
1 ATTTGGTACCTAAACTTGACA-TTTTTTCTA
* *
17412521 ATTTGGTACCTAAACTTTACACTTTTTCTGA
1 ATTTGGTACCTAAACTTGACATTTTTTCT-A
* *
17412552 AGTTGGTACTTAAACTT
1 ATTTGGTACCTAAACTT
17412569 TTTGGGGTCC
Statistics
Matches: 81, Mismatches: 18, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
26 4 0.05
27 16 0.20
30 6 0.07
31 51 0.63
32 4 0.05
ACGTcount: A:0.28, C:0.18, G:0.11, T:0.43
Consensus pattern (30 bp):
ATTTGGTACCTAAACTTGACATTTTTTCTA
Found at i:17412558 original size:89 final size:90
Alignment explanation
Indices: 17412432--17412619 Score: 229
Period size: 90 Copynumber: 2.1 Consensus size: 90
17412422 TTAATATAAT
* * *
17412432 ATTTGGTACCTAAACTTGACAATTTTTTCTAATTTGGTA-TCTAAACTTTTT-TGGTCCAATTAG
1 ATTTGGTACCTAAACTTGACAACTTTTTCTAAGTTGGTACT-TAAACTTTTTGGGGTCCAATTAG
*
17412495 ATACCCAAACTTGACACTTTTTCCTA
65 ATACACAAACTTGACACTTTTTCCTA
* *
17412521 ATTTGGTACCTAAACTTTAC-ACTTTTTCTGAAGTTGGTACTTAAACTTTTTGGGGTCCAATTTG
1 ATTTGGTACCTAAACTTGACAACTTTTTCT-AAGTTGGTACTTAAACTTTTTGGGGTCCAATTAG
* ** * *
17412585 GTACATGAACTTGACTCTTTTTCTTA
65 ATACACAAACTTGACACTTTTTCCTA
*
17412611 ATTCGGTAC
1 ATTTGGTAC
17412620 TTAATTTTTT
Statistics
Matches: 84, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
88 8 0.10
89 37 0.44
90 39 0.46
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.43
Consensus pattern (90 bp):
ATTTGGTACCTAAACTTGACAACTTTTTCTAAGTTGGTACTTAAACTTTTTGGGGTCCAATTAGA
TACACAAACTTGACACTTTTTCCTA
Found at i:17421153 original size:41 final size:40
Alignment explanation
Indices: 17421075--17421154 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 40
17421065 ATATTGAATG
*
17421075 CATGGAAAGCCAACATTCATAGCACAACCCACGCCCCCCA
1 CATGGAAAGCCAACATTCATAGCACAACCCACCCCCCCCA
* *
17421115 NCATGGAAAGCCAACATTCATAGCACACCCCCCCCCCCCC
1 -CATGGAAAGCCAACATTCATAGCACAACCCACCCCCCCC
17421155 CAAAGAGCTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.31, C:0.46, G:0.11, T:0.10
Consensus pattern (40 bp):
CATGGAAAGCCAACATTCATAGCACAACCCACCCCCCCCA
Found at i:17423061 original size:29 final size:31
Alignment explanation
Indices: 17423025--17423090 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 31
17423015 CCCTCTGTTA
** * *
17423025 TTTAAAATTTTTTCCTTATATT-TTTA-TTT
1 TTTAAAATTTAGTCCTTAAATTATTTAGATT
17423054 TTTAAAATTTAGTCCTTAAATTATTTAGATT
1 TTTAAAATTTAGTCCTTAAATTATTTAGATT
17423085 TTTAAA
1 TTTAAA
17423091 TTCAAGTTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 19 0.61
30 4 0.13
31 8 0.26
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (31 bp):
TTTAAAATTTAGTCCTTAAATTATTTAGATT
Found at i:17432032 original size:21 final size:20
Alignment explanation
Indices: 17432008--17432090 Score: 76
Period size: 21 Copynumber: 4.0 Consensus size: 20
17431998 CTCTCCCACG
* *
17432008 TCATCCCCTGGTTACAGCCC
1 TCATCTCCTGGCTACAGCCC
*
17432028 ATCATCTCCTGGCTACAGTCCT
1 -TCATCTCCTGGCTACAG-CCC
*
17432050 TCATCTCCTGGCTACAGTCC
1 TCATCTCCTGGCTACAGCCC
* * *
17432070 TACCTCGCCTGGTTACAGCCC
1 T-CATCTCCTGGCTACAGCCC
17432091 CACATCACCT
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
20 2 0.04
21 47 0.92
22 2 0.04
ACGTcount: A:0.16, C:0.41, G:0.16, T:0.28
Consensus pattern (20 bp):
TCATCTCCTGGCTACAGCCC
Found at i:17432209 original size:21 final size:21
Alignment explanation
Indices: 17432176--17432309 Score: 124
Period size: 21 Copynumber: 6.4 Consensus size: 21
17432166 TTATTCTCCA
* *
17432176 ACCTCACCGAGCTATAGCCCT
1 ACCTCACCAAGCTACAGCCCT
*
17432197 ACCTCTCCAAGCTACAGCCCT
1 ACCTCACCAAGCTACAGCCCT
* *
17432218 ACGTCTCCAAGCTACAGCCCT
1 ACCTCACCAAGCTACAGCCCT
* * * *
17432239 ACGTCTCCAAGTTACAGTCCT
1 ACCTCACCAAGCTACAGCCCT
* * * * *
17432260 ACTTCACCAAGTTATAGTCCA
1 ACCTCACCAAGCTACAGCCCT
*
17432281 ACTTCACCAAGCTACAGCCCT
1 ACCTCACCAAGCTACAGCCCT
*
17432302 ACTTCACC
1 ACCTCACC
17432310 GGCATATAGC
Statistics
Matches: 99, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 99 1.00
ACGTcount: A:0.26, C:0.40, G:0.11, T:0.22
Consensus pattern (21 bp):
ACCTCACCAAGCTACAGCCCT
Found at i:17432237 original size:42 final size:42
Alignment explanation
Indices: 17432179--17432309 Score: 145
Period size: 42 Copynumber: 3.1 Consensus size: 42
17432169 TTCTCCAACC
*
17432179 TCACCGAGCTATAGCCCTACCTCTCCAAGCTACAGCCCTACG
1 TCACCAAGCTATAGCCCTACCTCTCCAAGCTACAGCCCTACG
* * * * * *
17432221 TCTCCAAGCTACAGCCCTACGTCTCCAAGTTACAGTCCTACT
1 TCACCAAGCTATAGCCCTACCTCTCCAAGCTACAGCCCTACG
* * * * * *
17432263 TCACCAAGTTATAGTCCAACTTCACCAAGCTACAGCCCTACT
1 TCACCAAGCTATAGCCCTACCTCTCCAAGCTACAGCCCTACG
17432305 TCACC
1 TCACC
17432310 GGCATATAGC
Statistics
Matches: 73, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 73 1.00
ACGTcount: A:0.26, C:0.40, G:0.11, T:0.23
Consensus pattern (42 bp):
TCACCAAGCTATAGCCCTACCTCTCCAAGCTACAGCCCTACG
Found at i:17432318 original size:42 final size:42
Alignment explanation
Indices: 17432179--17432330 Score: 135
Period size: 42 Copynumber: 3.6 Consensus size: 42
17432169 TTCTCCAACC
* * * * * *
17432179 TCACCGAGCTATAGCCCTACCTCTCCAAGCTACAGCCCTACG
1 TCACCAAGATATAGCCCAACTTCACCAAGCTACAGCCCTACT
* * * * * * * *
17432221 TCTCCAAGCTACAGCCCTACGTCTCCAAGTTACAGTCCTACT
1 TCACCAAGATATAGCCCAACTTCACCAAGCTACAGCCCTACT
* *
17432263 TCACCAAGTTATAGTCCAACTTCACCAAGCTACAGCCCTACT
1 TCACCAAGATATAGCCCAACTTCACCAAGCTACAGCCCTACT
*
17432305 TCACC-GGCATATAGCCCAACTTCACC
1 TCACCAAG-ATATAGCCCAACTTCACC
17432331 TGCATACAGC
Statistics
Matches: 90, Mismatches: 19, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
41 1 0.01
42 89 0.99
ACGTcount: A:0.26, C:0.39, G:0.12, T:0.22
Consensus pattern (42 bp):
TCACCAAGATATAGCCCAACTTCACCAAGCTACAGCCCTACT
Found at i:17432320 original size:21 final size:21
Alignment explanation
Indices: 17432278--17432366 Score: 81
Period size: 21 Copynumber: 4.2 Consensus size: 21
17432268 AAGTTATAGT
*
17432278 CCAACTTCACCAAGC-TACAGC
1 CCAACTTCACC-GGCATACAGC
* *
17432299 CCTACTTCACCGGCATATAGC
1 CCAACTTCACCGGCATACAGC
*
17432320 CCAACTTCACCTGCATACAGC
1 CCAACTTCACCGGCATACAGC
* * * **
17432341 CCCACGTCTCCATCATACAGC
1 CCAACTTCACCGGCATACAGC
17432362 CCAAC
1 CCAAC
17432367 ATCGCCATCA
Statistics
Matches: 55, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 2 0.04
21 53 0.96
ACGTcount: A:0.28, C:0.44, G:0.10, T:0.18
Consensus pattern (21 bp):
CCAACTTCACCGGCATACAGC
Found at i:17432363 original size:42 final size:41
Alignment explanation
Indices: 17432312--17432477 Score: 143
Period size: 42 Copynumber: 4.0 Consensus size: 41
17432302 ACTTCACCGG
* *
17432312 CATATAGCCCAACTTCACCTGCATACAGCCCCACGTCTCCAT
1 CATACAGCCCAACTTCACCT-CATACAGCCCCACATCTCCAT
* * * * *
17432354 CATACAGCCCAACATCGCCATCATACAGTCCGACATCTCCTT
1 CATACAGCCCAACTTCACC-TCATACAGCCCCACATCTCCAT
* * * * *
17432396 CTTACAGCCCAACCTCACCCTCCTATAGCCCTACATCTCCAT
1 CATACAGCCCAACTTCA-CCTCATACAGCCCCACATCTCCAT
* * * * *
17432438 CATACAGCCCTACTTCCCCAGCATATAGCCCCACTTCTCC
1 CATACAGCCCAACTTCACC-TCATACAGCCCCACATCTCC
17432478 TGGGTACAGT
Statistics
Matches: 98, Mismatches: 23, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
41 2 0.02
42 93 0.95
43 3 0.03
ACGTcount: A:0.25, C:0.45, G:0.08, T:0.22
Consensus pattern (41 bp):
CATACAGCCCAACTTCACCTCATACAGCCCCACATCTCCAT
Found at i:17432450 original size:21 final size:21
Alignment explanation
Indices: 17432333--17432447 Score: 113
Period size: 21 Copynumber: 5.5 Consensus size: 21
17432323 ACTTCACCTG
* *
17432333 CATACAGCCCCACGTCTCCAT
1 CATACAGCCCAACATCTCCAT
*
17432354 CATACAGCCCAACATCGCCAT
1 CATACAGCCCAACATCTCCAT
* * *
17432375 CATACAGTCCGACATCTCCTT
1 CATACAGCCCAACATCTCCAT
* * * *
17432396 CTTACAGCCCAACCTCACCCT
1 CATACAGCCCAACATCTCCAT
* * *
17432417 CCTATAGCCCTACATCTCCAT
1 CATACAGCCCAACATCTCCAT
17432438 CATACAGCCC
1 CATACAGCCC
17432448 TACTTCCCCA
Statistics
Matches: 73, Mismatches: 21, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 73 1.00
ACGTcount: A:0.26, C:0.45, G:0.08, T:0.21
Consensus pattern (21 bp):
CATACAGCCCAACATCTCCAT
Found at i:17432462 original size:21 final size:21
Alignment explanation
Indices: 17432293--17432477 Score: 111
Period size: 21 Copynumber: 8.8 Consensus size: 21
17432283 TTCACCAAGC
* * **
17432293 TACAGCCCTACTTCACCGGCA
1 TACAGCCCAACTTCTCCATCA
* *
17432314 TATAGCCCAACTTCACC-TGCA
1 TACAGCCCAACTTCTCCAT-CA
* *
17432335 TACAGCCCCACGTCTCCATCA
1 TACAGCCCAACTTCTCCATCA
* *
17432356 TACAGCCCAACATCGCCATCA
1 TACAGCCCAACTTCTCCATCA
* * * * *
17432377 TACAGTCCGACATCTCCTTCT
1 TACAGCCCAACTTCTCCATCA
* * * *
17432398 TACAGCCCAACCTCACCCTCC
1 TACAGCCCAACTTCTCCATCA
* * *
17432419 TATAGCCCTACATCTCCATCA
1 TACAGCCCAACTTCTCCATCA
* * *
17432440 TACAGCCCTACTTCCCCAGCA
1 TACAGCCCAACTTCTCCATCA
* *
17432461 TATAGCCCCACTTCTCC
1 TACAGCCCAACTTCTCC
17432478 TGGGTACAGT
Statistics
Matches: 128, Mismatches: 34, Indels: 4
0.77 0.20 0.02
Matches are distributed among these distances:
21 127 0.99
22 1 0.01
ACGTcount: A:0.25, C:0.44, G:0.09, T:0.22
Consensus pattern (21 bp):
TACAGCCCAACTTCTCCATCA
Found at i:17432486 original size:84 final size:84
Alignment explanation
Indices: 17432338--17432498 Score: 187
Period size: 84 Copynumber: 1.9 Consensus size: 84
17432328 ACCTGCATAC
* * * * * * *
17432338 AGCCCCACGTCTCCATCATACAGCCCAACATCGCCATCATACAGTCCGACATCTCCTTCTTACAG
1 AGCCCCACATCTCCATCATACAGCCCAACATCCCCAGCATACAGCCCCACATCTCCTGCGTACAG
17432403 CCCAACCTCACCCTCCTAT
66 CCCAACCTCACCCTCCTAT
* * * * * *
17432422 AGCCCTACATCTCCATCATACAGCCCTACTTCCCCAGCATATAGCCCCACTTCTCCTGGGTACAG
1 AGCCCCACATCTCCATCATACAGCCCAACATCCCCAGCATACAGCCCCACATCTCCTGCGTACAG
* *
17432487 TCCGACCTCACC
66 CCCAACCTCACC
17432499 AAGTTACGGT
Statistics
Matches: 62, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
84 62 1.00
ACGTcount: A:0.24, C:0.45, G:0.10, T:0.22
Consensus pattern (84 bp):
AGCCCCACATCTCCATCATACAGCCCAACATCCCCAGCATACAGCCCCACATCTCCTGCGTACAG
CCCAACCTCACCCTCCTAT
Found at i:17442105 original size:59 final size:59
Alignment explanation
Indices: 17442040--17442227 Score: 150
Period size: 59 Copynumber: 3.2 Consensus size: 59
17442030 ATTTTATTAA
17442040 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATATTTTATAGT
* * ** * * * ** * * * *
17442099 ATCATATATTATGATTTTAGTA-AATTCATA-TAAGAATATTGATTATTAGAATTTTATTA-A
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCA-AATTA-TATTTTA-TAGT
* * * *
17442159 ATTATATATTTTAATTAAAATATATTTAATAATT-ATTATTTTAATTTATATTTTACAGT
1 ATCATATATTTTAATTAAAATATATTTAAT-ATTAATTATTTCAAATTATATTTTATAGT
17442218 ATCATATATT
1 ATCATATATT
17442228 ATGATTTGAG
Statistics
Matches: 91, Mismatches: 30, Indels: 16
0.66 0.22 0.12
Matches are distributed among these distances:
57 5 0.05
58 10 0.11
59 36 0.40
60 25 0.27
61 10 0.11
62 4 0.04
63 1 0.01
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.52
Consensus pattern (59 bp):
ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATATTTTATAGT
Found at i:17442154 original size:119 final size:120
Alignment explanation
Indices: 17442029--17442288 Score: 443
Period size: 119 Copynumber: 2.2 Consensus size: 120
17442019 AATTATTTTA
*
17442029 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAAT-ATTAATTATTTCAAATTATATTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATT-ATTATTTCAAATTATATTT
* * *
17442093 TATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATT-AG
65 TACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
17442148 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATTATTATTTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATTATTATTTCAAATTATATTTT
17442213 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
17442268 AATTTTATTAAATTATATATT
1 AATTTTATTAAATTATATATT
17442289 GGCTTCCAGT
Statistics
Matches: 133, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
119 107 0.80
120 26 0.20
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATTATTATTTCAAATTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:17442175 original size:18 final size:18
Alignment explanation
Indices: 17442149--17442204 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 18
17442139 GATTATTAGA
17442149 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAATTATAT
17442166 ATTTTAATTAAA--ATAT
1 ATTTTAATTAAATTATAT
17442182 A-TTTAA-T-AATTAT-T
1 ATTTTAATTAAATTATAT
17442196 ATTTTAATT
1 ATTTTAATT
17442205 TATATTTTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
13 2 0.06
14 3 0.09
15 12 0.35
16 6 0.18
17 5 0.15
18 6 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTTAATTAAATTATAT
Found at i:17442285 original size:59 final size:58
Alignment explanation
Indices: 17442103--17442285 Score: 146
Period size: 56 Copynumber: 3.1 Consensus size: 58
17442093 TATAGTATCA
*
17442103 TATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATT-AGAATTTTATTAAAT
1 TATATTATGATTTAAGTAAATTCATATAAGAATATT-ATTATTAAGAATTTTATTAAAT
* * * * * *
17442161 TATA-TAT--TTTAATTAAAATAT-ATTTAATAATTATTATT-TTAATTTATATTTTA-CAGTAT
1 TATATTATGATTTAAGT-AAAT-TCATATAAGAA-TATTATTATTAA--GA-ATTTTATTA-AAT
*
17442220 CATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
1 --TATATTATGATTTAAGTAAATTCATATAAGAATATT-ATTATTAAGAATTTTATTAAAT
17442281 TATAT
1 TATAT
17442286 ATTGGCTTCC
Statistics
Matches: 94, Mismatches: 14, Indels: 33
0.67 0.10 0.23
Matches are distributed among these distances:
55 7 0.07
56 15 0.16
57 8 0.09
58 6 0.06
59 13 0.14
61 12 0.13
62 10 0.11
63 14 0.15
64 9 0.10
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (58 bp):
TATATTATGATTTAAGTAAATTCATATAAGAATATTATTATTAAGAATTTTATTAAAT
Found at i:17442909 original size:42 final size:43
Alignment explanation
Indices: 17442874--17442989 Score: 128
Period size: 43 Copynumber: 2.7 Consensus size: 43
17442864 CGTTTTTGCT
* *
17442874 ACAAGCGTCGCTAAAGGT-TTGTTCTTTTGCAGCGTTTGTTAA
1 ACAAGCGTCGCTAAAGGTCATGTTCTTTAGCAGCGTTTGTTAA
* ** *
17442916 AGAAGCGTCGCTAAAGGTCATGTTCTTTAGTGGCGTTTGTGAGA
1 ACAAGCGTCGCTAAAGGTCATGTTCTTTAGCAGCGTTTGTTA-A
* * *
17442960 A-AAGCGCCGCTAAAGGTCTTGGTCTTTAGC
1 ACAAGCGTCGCTAAAGGTCATGTTCTTTAGC
17442990 GGCGCTTAAG
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
42 17 0.27
43 43 0.69
44 2 0.03
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (43 bp):
ACAAGCGTCGCTAAAGGTCATGTTCTTTAGCAGCGTTTGTTAA
Found at i:17442954 original size:43 final size:43
Alignment explanation
Indices: 17442854--17443038 Score: 162
Period size: 42 Copynumber: 4.3 Consensus size: 43
17442844 AAAGCTTATG
* ** *
17442854 TCTTTAGCGGCGTTTTTGCTACAAGCGTCGCTAAAGGT-TTGT
1 TCTTTAGCGGCGTTTGTGAGAAAAGCGTCGCTAAAGGTCTTGT
* * * *
17442896 TCTTTTGCAGCGTTTGTTA-AAGAAGCGTCGCTAAAGGTCATGT
1 TCTTTAGCGGCGTTTGTGAGAA-AAGCGTCGCTAAAGGTCTTGT
* * *
17442939 TCTTTAGTGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCTTGG
1 TCTTTAGCGGCGTTTGTGAGAAAAGCGTCGCTAAAGGTCTTGT
* ** * ** *
17442982 TCTTTAGCGGCGCTTAAGAAAAAATGC--CGCTAAAGACCATGT
1 TCTTTAGCGGCGTTTGTGAGAAAA-GCGTCGCTAAAGGTCTTGT
17443024 TCTTTAGCGGCGTTT
1 TCTTTAGCGGCGTTT
17443039 TTGTTTGTAA
Statistics
Matches: 115, Mismatches: 24, Indels: 8
0.78 0.16 0.05
Matches are distributed among these distances:
41 1 0.01
42 55 0.48
43 55 0.48
44 4 0.03
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (43 bp):
TCTTTAGCGGCGTTTGTGAGAAAAGCGTCGCTAAAGGTCTTGT
Found at i:17445374 original size:27 final size:28
Alignment explanation
Indices: 17445265--17445374 Score: 100
Period size: 27 Copynumber: 4.0 Consensus size: 28
17445255 TGTCTCATAC
*
17445265 CCATTGTTGTTGTAGTTG-TCATTGTAG
1 CCATTGTTGTTGTAGTTGCTCGTTGTAG
* * *
17445292 CCATTGGTGTTGTAG-TGCCCGCTGTAG
1 CCATTGTTGTTGTAGTTGCTCGTTGTAG
* * *
17445319 CCATTGTTGTTGTAGCTGCTGAGAGTGTAG
1 CCATTGTTGTTGTAGTTGCT-CG-TTGTAG
* *
17445349 CCATTGTTGTTGTTGTTG-TTGTTGTA
1 CCATTGTTGTTGTAGTTGCTCGTTGTA
17445375 ATAGTAGTTG
Statistics
Matches: 67, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
26 2 0.03
27 38 0.57
28 4 0.06
29 2 0.03
30 21 0.31
ACGTcount: A:0.13, C:0.14, G:0.30, T:0.44
Consensus pattern (28 bp):
CCATTGTTGTTGTAGTTGCTCGTTGTAG
Found at i:17450295 original size:25 final size:25
Alignment explanation
Indices: 17450267--17450317 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
17450257 TCTTCCCAGA
17450267 TGAATAACGGGAAGCTCATGCGAGC
1 TGAATAACGGGAAGCTCATGCGAGC
*
17450292 TGAATAACGGGAAGCTCATGTGAGC
1 TGAATAACGGGAAGCTCATGCGAGC
17450317 T
1 T
17450318 AAGTATTGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.31, T:0.20
Consensus pattern (25 bp):
TGAATAACGGGAAGCTCATGCGAGC
Found at i:17457074 original size:26 final size:27
Alignment explanation
Indices: 17457027--17457082 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
17457017 TTAATTTTAA
*
17457027 AAAATTACAAACCGAATCAAGTGAAAT
1 AAAATTACAAACCGAATAAAGTGAAAT
* * *
17457054 AAAATT-CAAATCGAGTAAAGTTAAAT
1 AAAATTACAAACCGAATAAAGTGAAAT
17457080 AAA
1 AAA
17457083 TTTATTTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 19 0.76
27 6 0.24
ACGTcount: A:0.57, C:0.11, G:0.11, T:0.21
Consensus pattern (27 bp):
AAAATTACAAACCGAATAAAGTGAAAT
Found at i:17462004 original size:27 final size:27
Alignment explanation
Indices: 17461966--17462022 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
17461956 GAAACCAGAG
17461966 TGATTGTTTTCTCAGCTGCATCAAAGT
1 TGATTGTTTTCTCAGCTGCATCAAAGT
17461993 TGATTGTTTTCTCAGCTGCATCAAAGT
1 TGATTGTTTTCTCAGCTGCATCAAAGT
17462020 TGA
1 TGA
17462023 GTGAGTGTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (27 bp):
TGATTGTTTTCTCAGCTGCATCAAAGT
Found at i:17471239 original size:1 final size:1
Alignment explanation
Indices: 17471233--17471261 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
17471223 GCTCCAAAGG
17471233 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
17471262 CTTTCCCCCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:17479274 original size:8 final size:8
Alignment explanation
Indices: 17479261--17479291 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
17479251 CTTTCACTAA
17479261 TTTAAAAT
1 TTTAAAAT
17479269 TTTAAAAT
1 TTTAAAAT
17479277 TTTAAAAT
1 TTTAAAAT
17479285 TTTAAAA
1 TTTAAAA
17479292 GGCCTAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
TTTAAAAT
Found at i:17481212 original size:67 final size:65
Alignment explanation
Indices: 17481140--17481271 Score: 160
Period size: 67 Copynumber: 2.0 Consensus size: 65
17481130 TATATATAAA
17481140 CCCACTCATATATA-TATTATAAAAAAAC-CCAAACTCACGCATATATATATGTTTAACACCAAC
1 CCCACTCATATATATTA-TAT-AAAAAACTCCAAACTCACGCATATATATA--TTTAACACCAAC
17481203 AGAC
62 AGAC
** ** * *
17481207 CCCACTCATATATATTATATTTATGACTCCAATCTCACGCATATATATATTTAACACCTACAGAC
1 CCCACTCATATATATTATATAAAAAACTCCAAACTCACGCATATATATATTTAACACCAACAGAC
17481272 TCGTGCATCT
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
65 15 0.26
66 3 0.05
67 37 0.65
68 2 0.04
ACGTcount: A:0.40, C:0.26, G:0.05, T:0.30
Consensus pattern (65 bp):
CCCACTCATATATATTATATAAAAAACTCCAAACTCACGCATATATATATTTAACACCAACAGAC
Found at i:17481218 original size:65 final size:66
Alignment explanation
Indices: 17481140--17481271 Score: 162
Period size: 65 Copynumber: 2.0 Consensus size: 66
17481130 TATATATAAA
17481140 CCCACTCATATATATATTATA-AAAAAAC-CCAAACTCACGCATATATATATGTTTAACACCAAC
1 CCCACTCA-ATATATATTATATAAAAAACTCCAAACTCACGCATATATATA--TTTAACACCAAC
17481203 AGAC
63 AGAC
** ** * *
17481207 CCCACTC-ATATATATTATATTTATGACTCCAATCTCACGCATATATATATTTAACACCTACAGA
1 CCCACTCAATATATATTATATAAAAAACTCCAAACTCACGCATATATATATTTAACACCAACAGA
17481271 C
66 C
17481272 TCGTGCATCT
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
65 27 0.47
66 3 0.05
67 27 0.47
ACGTcount: A:0.40, C:0.26, G:0.05, T:0.30
Consensus pattern (66 bp):
CCCACTCAATATATATTATATAAAAAACTCCAAACTCACGCATATATATATTTAACACCAACAGA
C
Found at i:17483190 original size:18 final size:19
Alignment explanation
Indices: 17483167--17483205 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
17483157 GTTTTCTTCG
17483167 AATTTTA-AATATTTTCAA
1 AATTTTATAATATTTTCAA
* *
17483185 AATTTTATAATTTTTTTAA
1 AATTTTATAATATTTTCAA
17483204 AA
1 AA
17483206 AATATGTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (19 bp):
AATTTTATAATATTTTCAA
Found at i:17483262 original size:32 final size:31
Alignment explanation
Indices: 17483197--17483258 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
17483187 TTTTATAATT
* *
17483197 TTTTTAAAAAATATGTACTTATTTTTTTTAA
1 TTTTTAAAAAATATGTAATTATTTTTTTAAA
17483228 TTTTTAATAAAATAT-TAATT-TTTTTTCTAAA
1 TTTTTAA-AAAATATGTAATTATTTTTT-TAAA
17483259 ATTTATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 6 0.22
31 14 0.52
32 7 0.26
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (31 bp):
TTTTTAAAAAATATGTAATTATTTTTTTAAA
Found at i:17494171 original size:19 final size:21
Alignment explanation
Indices: 17494130--17494172 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
17494120 TTTAACCAAT
17494130 TCAAAACACGATCAAATACAA
1 TCAAAACACGATCAAATACAA
*
17494151 TCAAAACATG-TCAAA-ACAA
1 TCAAAACACGATCAAATACAA
17494170 TCA
1 TCA
17494173 TCTTAGGTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.33
20 5 0.24
21 9 0.43
ACGTcount: A:0.56, C:0.23, G:0.05, T:0.16
Consensus pattern (21 bp):
TCAAAACACGATCAAATACAA
Found at i:17496462 original size:43 final size:43
Alignment explanation
Indices: 17496406--17496566 Score: 227
Period size: 43 Copynumber: 3.7 Consensus size: 43
17496396 ATTTGAGATC
17496406 TACGTGTAAGACCATGTCTGGGACATTGGCATCGTATATGATT
1 TACGTGTAAGACCATGTCTGGGACATTGGCATCGTATATGATT
17496449 TACGTGTAAGACCATGTCTGGGACATTGGCATCGTATATGATT
1 TACGTGTAAGACCATGTCTGGGACATTGGCATCGTATATGATT
* * * *
17496492 TACGTGTCAGACCATGTCTAGGACAGTGGCATCGATATTTGA-T
1 TACGTGTAAGACCATGTCTGGGACATTGGCATCG-TATATGATT
* * *
17496535 TACATGCAAGACC-TCGTCTGGGACATAGGCAT
1 TACGTGTAAGACCAT-GTCTGGGACATTGGCAT
17496567 TGTAAGATCT
Statistics
Matches: 106, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
42 1 0.01
43 99 0.93
44 6 0.06
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (43 bp):
TACGTGTAAGACCATGTCTGGGACATTGGCATCGTATATGATT
Found at i:17504133 original size:43 final size:43
Alignment explanation
Indices: 17504074--17504191 Score: 191
Period size: 43 Copynumber: 2.7 Consensus size: 43
17504064 ATTTGAGATC
*
17504074 TACGTGTAAGACCATGTTTGGGACATTGGCATCGTATATGATT
1 TACGTGTAAGACCATGTCTGGGACATTGGCATCGTATATGATT
* *
17504117 TACGTGTAAGATCATGTCTGGGACATTGGCTTCGTATATGATT
1 TACGTGTAAGACCATGTCTGGGACATTGGCATCGTATATGATT
* *
17504160 TACGTGTAAGACCCTGTCTGGGACAGTGGCAT
1 TACGTGTAAGACCATGTCTGGGACATTGGCAT
17504192 TGATATTTGA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 68 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (43 bp):
TACGTGTAAGACCATGTCTGGGACATTGGCATCGTATATGATT
Found at i:17504215 original size:43 final size:43
Alignment explanation
Indices: 17504037--17504203 Score: 178
Period size: 43 Copynumber: 3.8 Consensus size: 43
17504027 AATATTGTGA
* * *
17504037 AAGACCACGTCTGGGAC-GATGGCATTG-ATTTGAGATCTACGTGT
1 AAGACCATGTCTGGGACAG-TGGCATTGTATAT--GATTTACGTGT
* * *
17504081 AAGACCATGTTTGGGACATTGGCATCGTATATGATTTACGTGT
1 AAGACCATGTCTGGGACAGTGGCATTGTATATGATTTACGTGT
* *
17504124 AAGATCATGTCTGGGACATTGGC-TTCGTATATGATTTACGTGT
1 AAGACCATGTCTGGGACAGTGGCATT-GTATATGATTTACGTGT
* *
17504167 AAGACCCTGTCTGGGACAGTGGCATTGATATTTGATT
1 AAGACCATGTCTGGGACAGTGGCATTG-TATATGATT
17504204 ACATGCAAGA
Statistics
Matches: 105, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
42 1 0.01
43 69 0.66
44 32 0.30
45 3 0.03
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.33
Consensus pattern (43 bp):
AAGACCATGTCTGGGACAGTGGCATTGTATATGATTTACGTGT
Found at i:17506295 original size:23 final size:23
Alignment explanation
Indices: 17506269--17506312 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
17506259 ATGTATTCAA
*
17506269 TATATTCATATGTATAACTAACT
1 TATATGCATATGTATAACTAACT
* *
17506292 TATATGCATATTTATACCTAA
1 TATATGCATATGTATAACTAA
17506313 AGTTTACCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.39, C:0.14, G:0.05, T:0.43
Consensus pattern (23 bp):
TATATGCATATGTATAACTAACT
Found at i:17507212 original size:62 final size:62
Alignment explanation
Indices: 17507109--17507239 Score: 244
Period size: 62 Copynumber: 2.1 Consensus size: 62
17507099 CATCAAACAA
17507109 CAACACTTGTTAGCATACTTGAACATATTTCATATAAATTCAACATCGATAACCTTATTATCT
1 CAACA-TTGTTAGCATACTTGAACATATTTCATATAAATTCAACATCGATAACCTTATTATCT
*
17507172 CAACATTGTTAGCATACTTGAACATATTTCCTATAAATTCAACATCGATAACCTTATTATCT
1 CAACATTGTTAGCATACTTGAACATATTTCATATAAATTCAACATCGATAACCTTATTATCT
17507234 CAACAT
1 CAACAT
17507240 GTCACACTTG
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
62 62 0.93
63 5 0.07
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.36
Consensus pattern (62 bp):
CAACATTGTTAGCATACTTGAACATATTTCATATAAATTCAACATCGATAACCTTATTATCT
Found at i:17512302 original size:21 final size:21
Alignment explanation
Indices: 17512276--17512408 Score: 106
Period size: 21 Copynumber: 6.3 Consensus size: 21
17512266 CAGACACGTC
* *
17512276 AACAGAAGCTCATAAGAGTTG
1 AACAGAAGCTCATAAGAGCTA
*
17512297 AACAGAAGCTCGTAAGAGCTA
1 AACAGAAGCTCATAAGAGCTA
** *** *
17512318 AACACCAGCTCGGCAGAGCTC
1 AACAGAAGCTCATAAGAGCTA
* ** * *
17512339 AACAAAAATTCATAAGAGTTG
1 AACAGAAGCTCATAAGAGCTA
* *
17512360 AACAGAAGCTCGTAAGAACTA
1 AACAGAAGCTCATAAGAGCTA
17512381 AACAGAAGCTCGA-AAGAGCTA
1 AACAGAAGCTC-ATAAGAGCTA
17512402 AACAGAA
1 AACAGAA
17512409 AGAAAAACAC
Statistics
Matches: 85, Mismatches: 26, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
21 85 1.00
ACGTcount: A:0.45, C:0.20, G:0.21, T:0.14
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTA
Found at i:17512399 original size:63 final size:63
Alignment explanation
Indices: 17512285--17512405 Score: 188
Period size: 63 Copynumber: 1.9 Consensus size: 63
17512275 CAACAGAAGC
* * ** *
17512285 TCATAAGAGTTGAACAGAAGCTCGTAAGAGCTAAACACCAGCTCGGCAGAGCTCAACAAAAAT
1 TCATAAGAGTTGAACAGAAGCTCGTAAGAACTAAACACAAGCTCGAAAGAGCTAAACAAAAAT
*
17512348 TCATAAGAGTTGAACAGAAGCTCGTAAGAACTAAACAGAAGCTCGAAAGAGCTAAACA
1 TCATAAGAGTTGAACAGAAGCTCGTAAGAACTAAACACAAGCTCGAAAGAGCTAAACA
17512406 GAAAGAAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 52 1.00
ACGTcount: A:0.44, C:0.20, G:0.21, T:0.16
Consensus pattern (63 bp):
TCATAAGAGTTGAACAGAAGCTCGTAAGAACTAAACACAAGCTCGAAAGAGCTAAACAAAAAT
Found at i:17517804 original size:46 final size:46
Alignment explanation
Indices: 17517726--17517909 Score: 314
Period size: 46 Copynumber: 4.0 Consensus size: 46
17517716 ATTGATATAG
* * *
17517726 CTCAGTATGGTTTTCTTTACGGAAATACCATACCTACTTTTCACAA
1 CTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACAA
*
17517772 CTCAGTATGGTTTTCTTCACTGAAACATCATACCTACTTTTCACAA
1 CTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACAA
17517818 CTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACAA
1 CTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACAA
* *
17517864 CTCAGTATGGCTTTCTTCACTGAAACACCAGACCTACTTTTCACAA
1 CTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACAA
17517910 TTTTCCATGG
Statistics
Matches: 131, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 131 1.00
ACGTcount: A:0.28, C:0.27, G:0.10, T:0.35
Consensus pattern (46 bp):
CTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCACAA
Found at i:17519156 original size:17 final size:17
Alignment explanation
Indices: 17519134--17519166 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
17519124 AAATTCTTTT
17519134 TAAATCACAAAATTCAA
1 TAAATCACAAAATTCAA
*
17519151 TAAATCACAAATTTCA
1 TAAATCACAAAATTCA
17519167 CTAATTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAATCACAAAATTCAA
Found at i:17520920 original size:42 final size:42
Alignment explanation
Indices: 17520857--17520951 Score: 154
Period size: 42 Copynumber: 2.3 Consensus size: 42
17520847 ATATGAACGA
* *
17520857 CACTAAGTGTGCGAAACTAAAATGACGATGTTGAATAATGGG
1 CACTAAGTGTGCGAAACTAAAATGACAATGTTGAATAACGGG
* *
17520899 CACTAAGTGTGCGAAATTAAAATGATAATGTTGAATAACGGG
1 CACTAAGTGTGCGAAACTAAAATGACAATGTTGAATAACGGG
17520941 CACTAAGTGTG
1 CACTAAGTGTG
17520952 AGATACCGAG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (42 bp):
CACTAAGTGTGCGAAACTAAAATGACAATGTTGAATAACGGG
Found at i:17533614 original size:28 final size:28
Alignment explanation
Indices: 17533583--17533638 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
17533573 GTTCTCTATT
17533583 TCCCCATCCATTTTTATTCATTTTTCAC
1 TCCCCATCCATTTTTATTCATTTTTCAC
*
17533611 TCCCCATTCATTTTTATTCATTTTTCAC
1 TCCCCATCCATTTTTATTCATTTTTCAC
17533639 ACTTCTAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.18, C:0.30, G:0.00, T:0.52
Consensus pattern (28 bp):
TCCCCATCCATTTTTATTCATTTTTCAC
Found at i:17533987 original size:18 final size:18
Alignment explanation
Indices: 17533956--17533990 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17533946 TATATTATAA
17533956 TATTAATTAATAAAATAT
1 TATTAATTAATAAAATAT
* *
17533974 TATTACTTATTAAAATA
1 TATTAATTAATAAAATA
17533991 ACATTTAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
TATTAATTAATAAAATAT
Found at i:17535818 original size:2 final size:2
Alignment explanation
Indices: 17535811--17535856 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
17535801 CTGCATCTTC
17535811 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
17535853 CT CT
1 CT CT
17535857 TTTCCCAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:17541809 original size:19 final size:18
Alignment explanation
Indices: 17541785--17541825 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
17541775 GTTTATTGTA
* *
17541785 TTCTCTTTTTTATTTTCTT
1 TTCTCTCTTCTATTTT-TT
17541804 TTCTCTCTTCTATTTTTT
1 TTCTCTCTTCTATTTTTT
17541822 TTCT
1 TTCT
17541826 GTTCTCTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.76
Consensus pattern (18 bp):
TTCTCTCTTCTATTTTTT
Found at i:17544031 original size:24 final size:25
Alignment explanation
Indices: 17544003--17544055 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
17543993 AAGTTCAAGC
17544003 GAGCTAA-TATCGGGAAGCT-ATGAA
1 GAGCTAATTATCGGGAAGCTCAT-AA
17544027 GAGCTAATTATCGGGAAGCTCATAA
1 GAGCTAATTATCGGGAAGCTCATAA
17544052 GAGC
1 GAGC
17544056 CATAAATAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
24 7 0.26
25 18 0.67
26 2 0.07
ACGTcount: A:0.36, C:0.15, G:0.28, T:0.21
Consensus pattern (25 bp):
GAGCTAATTATCGGGAAGCTCATAA
Found at i:17545899 original size:36 final size:35
Alignment explanation
Indices: 17545850--17545917 Score: 84
Period size: 36 Copynumber: 1.9 Consensus size: 35
17545840 AAAAGTTGAG
*
17545850 ACAAACCACGTATATGAT-AAAATAGGGTTTTAAGAT
1 ACAAACCACGTATA-AATAAAAATA-GGTTTTAAGAT
* *
17545886 ACAAATCATGTATAAATAAAAATAGGTTTTAA
1 ACAAACCACGTATAAATAAAAATAGGTTTTAA
17545918 AATTATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
35 10 0.36
36 18 0.64
ACGTcount: A:0.49, C:0.09, G:0.13, T:0.29
Consensus pattern (35 bp):
ACAAACCACGTATAAATAAAAATAGGTTTTAAGAT
Found at i:17546193 original size:20 final size:21
Alignment explanation
Indices: 17546168--17546207 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
17546158 GATTTTAAAG
17546168 AATAATACAT-TAT-AAAATAT
1 AATAATA-ATATATGAAAATAT
17546188 AATAATAATATATGAAAATA
1 AATAATAATATATGAAAATA
17546208 ATATAAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.11
20 10 0.56
21 6 0.33
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (21 bp):
AATAATAATATATGAAAATAT
Found at i:17546915 original size:21 final size:21
Alignment explanation
Indices: 17546889--17546930 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
17546879 TTCTTTTAAA
**
17546889 ATTTTTTGATTTCTTTCGTAT
1 ATTTTTTGATTGATTTCGTAT
*
17546910 ATTTTTTTATTGATTTCGTAT
1 ATTTTTTGATTGATTTCGTAT
17546931 TGTCCGTGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.07, G:0.10, T:0.67
Consensus pattern (21 bp):
ATTTTTTGATTGATTTCGTAT
Found at i:17560454 original size:27 final size:27
Alignment explanation
Indices: 17560423--17560476 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
17560413 TCTTTAAATT
* *
17560423 AATATTAATTTATCGATAAATTAATAA
1 AATATTAATTTATCAATAAACTAATAA
*
17560450 AATATTCATTTATCAATAAACTAATAA
1 AATATTAATTTATCAATAAACTAATAA
17560477 CCTCGATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (27 bp):
AATATTAATTTATCAATAAACTAATAA
Found at i:17562529 original size:18 final size:17
Alignment explanation
Indices: 17562508--17562542 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
17562498 TTATTATTAA
*
17562508 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
17562526 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
17562543 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:17562596 original size:157 final size:157
Alignment explanation
Indices: 17562395--17562711 Score: 580
Period size: 157 Copynumber: 2.0 Consensus size: 157
17562385 TAGAATACCC
*
17562395 TTAGCATAAATTTGTTTTGGTAAATGATTATTATTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTATTATTGTTATTTAAATTTTAATAAGATTATTA
* * *
17562460 TTATCAATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
17562525 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
* *
17562552 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTATTATTGTTATTTAAATTTTAATAAGATTATTA
17562617 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
17562682 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
17562709 TTA
1 TTA
17562712 ATATTCTTAT
Statistics
Matches: 154, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
157 154 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (157 bp):
TTAGCAGAAATTTGTTTTGGTAAATGATTATTATTATTGTTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:17562682 original size:16 final size:16
Alignment explanation
Indices: 17562645--17562686 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
17562635 TTAATCATAT
*
17562645 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
17562661 TT-AAATATATTATAA
1 TTAAAATATATTATAA
17562676 TTAAAATATAT
1 TTAAAATATAT
17562687 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:17562693 original size:14 final size:15
Alignment explanation
Indices: 17562654--17562695 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
17562644 TTTAAACATA
*
17562654 ATTATTATTAAATAT
1 ATTATAATTAAATAT
17562669 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
17562683 A-TATAATTTAATA
1 ATTATAATTAAATA
17562696 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:17562708 original size:82 final size:82
Alignment explanation
Indices: 17562465--17562714 Score: 215
Period size: 76 Copynumber: 3.1 Consensus size: 82
17562455 TATTATTATC
* *
17562465 AATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATAT
1 AATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATAT
17562530 AATTTAATAAAATTCTT
66 AATTTAATAAAATTCTT
* * * *
17562547 AATAATTAGCAGA-AATTT-GT--T-TTGGT-AA-ATTATTATTGTT--AT-TGTTAT--TTAAA
1 AATAA-TA--A-ATAATTTAATCATATT--TAAACATAATTATTATTAAATATATTATAATTAAA
* * * * *
17562600 TTTTAATAAGATTATTAATA-TC--
60 ATAT-ATAA-TTTAATAAAATTCTT
17562622 AATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATAT
1 AATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATAT
17562687 AATTTAATAAAATTCTT
66 AATTTAATAAAATTCTT
*
17562704 AATAATTAATA
1 AATAATAAATA
17562715 TTCTTATATG
Statistics
Matches: 124, Mismatches: 21, Indels: 46
0.65 0.11 0.24
Matches are distributed among these distances:
71 1 0.01
72 6 0.05
73 1 0.01
74 3 0.02
75 8 0.06
76 19 0.15
77 6 0.05
78 13 0.10
79 14 0.11
80 6 0.05
81 19 0.15
82 18 0.15
83 3 0.02
84 1 0.01
85 5 0.04
86 1 0.01
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (82 bp):
AATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATAT
AATTTAATAAAATTCTT
Found at i:17562783 original size:120 final size:119
Alignment explanation
Indices: 17562643--17562938 Score: 483
Period size: 120 Copynumber: 2.5 Consensus size: 119
17562633 ATTTAATCAT
*
17562643 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
17562708 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAAT-ATAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATAC--T-AAATGA-AA
17562765 A-TT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
17562828 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTAAATGAAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTAAATGAAA
* * * *
17562882 ATTTGAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATACAATT
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
17562939 TAAAATAATT
Statistics
Matches: 167, Mismatches: 4, Indels: 10
0.92 0.02 0.06
Matches are distributed among these distances:
117 7 0.04
118 50 0.30
119 2 0.01
120 105 0.63
121 2 0.01
122 1 0.01
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (119 bp):
ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTAAATGAAA
Found at i:17562813 original size:14 final size:15
Alignment explanation
Indices: 17562764--17562815 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
17562754 GTAAAATATA
17562764 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
17562779 TATTAAATATATTAT
1 AATTAAATATATTAT
17562794 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
17562807 AATTTAATA
1 AATTAAATA
17562816 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:17573092 original size:16 final size:16
Alignment explanation
Indices: 17573071--17573102 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
17573061 AGGCGGCATC
17573071 AATGGTGTCAGTGGCA
1 AATGGTGTCAGTGGCA
17573087 AATGGTGTCAGTGGCA
1 AATGGTGTCAGTGGCA
17573103 GAGGCGGCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.12, G:0.38, T:0.25
Consensus pattern (16 bp):
AATGGTGTCAGTGGCA
Found at i:17573120 original size:27 final size:28
Alignment explanation
Indices: 17573085--17573139 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
17573075 GTGTCAGTGG
* * * *
17573085 CAAATGGTGTCAGTGGCAGAGGCGGCAC
1 CAAATGGTGCCACTGCCACAGGCGGCAC
17573113 CAAA-GGTGCCACTGCCACAGGCGGCAC
1 CAAATGGTGCCACTGCCACAGGCGGCAC
17573140 TCTCTCTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.25, C:0.29, G:0.35, T:0.11
Consensus pattern (28 bp):
CAAATGGTGCCACTGCCACAGGCGGCAC
Found at i:17573283 original size:34 final size:31
Alignment explanation
Indices: 17573222--17573293 Score: 81
Period size: 34 Copynumber: 2.2 Consensus size: 31
17573212 ATATGTTTAT
17573222 GAAAAAATAAATACGAAAAGAAATAAAAAAC
1 GAAAAAATAAATACGAAAAGAAATAAAAAAC
* * **
17573253 GAAAACAATAAATTTACGGAAAGTAATAAAATTC
1 GAAAA-AATAAA--TACGAAAAGAAATAAAAAAC
17573287 GAAAAAA
1 GAAAAAA
17573294 AAGAAAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
31 5 0.15
32 6 0.18
33 2 0.06
34 21 0.62
ACGTcount: A:0.67, C:0.07, G:0.11, T:0.15
Consensus pattern (31 bp):
GAAAAAATAAATACGAAAAGAAATAAAAAAC
Found at i:17573438 original size:161 final size:158
Alignment explanation
Indices: 17573271--17573634 Score: 536
Period size: 161 Copynumber: 2.3 Consensus size: 158
17573261 TAAATTTACG
*
17573271 GAAAGTAATAAAATTCGAAAAAAAAGAAAAATACGAACAAA-TGGCCAAAATAAGG-GTTTTTCA
1 GAAAGTAATAAAATTCGAAAAAAAAGAAAAATACGAACAAAGT-GCCAAAATAAGGACTTTTT-A
* * *
17573334 CTAATTTTTTTTATAAAAAACACACTAA-AATAATACATTTCAAACATTATTTACTAAAATAATA
64 CTAA--ATTTATAT-AAAAACACAC-AACAATAATACATTTCAAACATTATGTACTAAAATAATA
17573398 TAAAATAATAAAATACAAAAATAATATATTTTTT
125 TAAAATAATAAAATACAAAAATAATATATTTTTT
*
17573432 GAAAGTAATAAAATTTGAAAAAAAAATAGAAAAATACGAACAAAGTGCCAAAATAAGGACTTTTT
1 GAAAGTAATAAAATTCG--AAAAAAA-AGAAAAATACGAACAAAGTGCCAAAATAAGGACTTTTT
*
17573497 ACTAAATTTATATAAAAACACACAACAATAATACATTTCAAACTTTATGTACTAAAATAATATAA
63 ACTAAATTTATATAAAAACACACAACAATAATACATTTCAAACATTATGTACTAAAATAATATAA
*
17573562 AATAATAAAATACAAAAATAGTATATTTTTT
128 AATAATAAAATACAAAAATAATATATTTTTT
* * *
17573593 AAAAGTAATAAAATCCGAAAAAAGAGAAAAATACGAACAAAG
1 GAAAGTAATAAAATTCGAAAAAAAAGAAAAATACGAACAAAG
17573635 GGGGTGCCGC
Statistics
Matches: 186, Mismatches: 11, Indels: 15
0.88 0.05 0.07
Matches are distributed among these distances:
158 18 0.10
159 6 0.03
160 2 0.01
161 107 0.58
162 6 0.03
163 7 0.04
164 34 0.18
165 6 0.03
ACGTcount: A:0.56, C:0.09, G:0.07, T:0.27
Consensus pattern (158 bp):
GAAAGTAATAAAATTCGAAAAAAAAGAAAAATACGAACAAAGTGCCAAAATAAGGACTTTTTACT
AAATTTATATAAAAACACACAACAATAATACATTTCAAACATTATGTACTAAAATAATATAAAAT
AATAAAATACAAAAATAATATATTTTTT
Found at i:17574151 original size:11 final size:12
Alignment explanation
Indices: 17574130--17574154 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17574120 GCTTGTACTA
17574130 TTTTAATTTTTT
1 TTTTAATTTTTT
17574142 TTTTAATTTTTT
1 TTTTAATTTTTT
17574154 T
1 T
17574155 GTATTATTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTAATTTTTT
Found at i:17576481 original size:49 final size:49
Alignment explanation
Indices: 17576385--17576482 Score: 144
Period size: 49 Copynumber: 2.0 Consensus size: 49
17576375 GTTTCATACT
* **
17576385 TTGGCTTTAAACAAGTATGACAAAGAAGCATAATGAAAATTTTACTTAA
1 TTGGATTTAAACAAGTATGACAAAGAAGCATAATGAAAATTGCACTTAA
*
17576434 TTGGATTTAAACAAGTATGA-AACAGAAGTATAATGAAAATTGCACTTAA
1 TTGGATTTAAACAAGTATGACAA-AGAAGCATAATGAAAATTGCACTTAA
17576483 GTTCAGCTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
48 2 0.05
49 42 0.95
ACGTcount: A:0.46, C:0.09, G:0.15, T:0.30
Consensus pattern (49 bp):
TTGGATTTAAACAAGTATGACAAAGAAGCATAATGAAAATTGCACTTAA
Found at i:17578137 original size:16 final size:16
Alignment explanation
Indices: 17578116--17578183 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
17578106 TTTGGTTCGC
17578116 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
17578132 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
17578148 TGTAATGGATTAGAGG
1 TGTATTGGATTAGAGG
*
17578164 TGTATTGGAATAGAGG
1 TGTATTGGATTAGAGG
17578180 TGTA
1 TGTA
17578184 ATAGCAAATC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:17578223 original size:45 final size:41
Alignment explanation
Indices: 17578164--17578273 Score: 116
Period size: 45 Copynumber: 2.6 Consensus size: 41
17578154 GGATTAGAGG
*
17578164 TGTATTGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGG-T
* * ***
17578206 GAATGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGT
1 ---TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGT
17578249 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
17578274 TAATGGAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
39 20 0.36
40 2 0.04
43 1 0.02
44 11 0.20
45 22 0.39
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (41 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGT
Found at i:17578436 original size:16 final size:16
Alignment explanation
Indices: 17578399--17578440 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
17578389 TTAATCATAT
*
17578399 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
17578415 TT-AAATATATTATAA
1 TTAAAATATATTATAA
17578430 TTAAAATATAT
1 TTAAAATATAT
17578441 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:17578447 original size:14 final size:15
Alignment explanation
Indices: 17578408--17578449 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
17578398 TTTAAACATA
*
17578408 ATTATTATTAAATAT
1 ATTATAATTAAATAT
17578423 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
17578437 A-TATAATTTAATA
1 ATTATAATTAAATA
17578450 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:17578499 original size:61 final size:61
Alignment explanation
Indices: 17578434--17578621 Score: 208
Period size: 61 Copynumber: 3.1 Consensus size: 61
17578424 TTATAATTAA
17578434 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
* * * * * * * * * *
17578495 AATATATGATACT-ATAAAA-TATAAATTAA-C-ATAATTATTAT-TAAATATA-TTATAATTAA
1 AATATATAAT-TTAATAAAATTCTTAA-TAATCAAT-ATTCTTATATGAATTTACTCA-AATCAT
17578554 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
17578615 AATATAT
1 AATATAT
17578622 GATACTATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 20
0.71 0.15 0.15
Matches are distributed among these distances:
58 3 0.03
59 30 0.31
60 24 0.25
61 37 0.38
62 3 0.03
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
Found at i:17578547 original size:120 final size:120
Alignment explanation
Indices: 17578402--17578631 Score: 460
Period size: 120 Copynumber: 1.9 Consensus size: 120
17578392 ATCATATTTA
17578402 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
17578467 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
17578522 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
17578587 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAA
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAA
17578632 TTTACTCAAA
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 110 1.00
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.42
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
Found at i:17578567 original size:14 final size:15
Alignment explanation
Indices: 17578518--17578569 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
17578508 ATAAAATATA
17578518 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
17578533 TATTAAATATATTAT
1 AATTAAATATATTAT
17578548 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
17578561 AATTTAATA
1 AATTAAATA
17578570 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:17578620 original size:59 final size:59
Alignment explanation
Indices: 17578437--17578620 Score: 175
Period size: 59 Copynumber: 3.1 Consensus size: 59
17578427 TAATTAAAAT
17578437 ATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATA
1 ATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATA
* * * * * * *
17578496 ATAT-ATGATACTATAAAA-TATAAATTAA-CATAATTATTATTAAAT-ATATTATAATTAAA--
1 ATATAAT-TTA--ATAAAATTCTTAA-TAATC--AA-TATTCTTATATGA-ATT-TACTCAAATC
17578555 AT-
57 ATA
17578557 ATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATA
1 ATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATA
17578616 ATATA
1 ATATA
17578621 TGATACTATA
Statistics
Matches: 95, Mismatches: 14, Indels: 32
0.67 0.10 0.23
Matches are distributed among these distances:
56 6 0.06
57 12 0.13
58 7 0.07
59 20 0.21
60 10 0.11
61 15 0.16
62 7 0.07
63 12 0.13
64 6 0.06
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.42
Consensus pattern (59 bp):
ATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATA
Found at i:17582336 original size:30 final size:31
Alignment explanation
Indices: 17582282--17582339 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
17582272 TTTTTTTGTC
*
17582282 ATTAAACTATTTGAAAGTTTTTATTTAAGTT
1 ATTAAACTATTTGAAAGATTTTATTTAAGTT
*
17582313 ATTAAATTATTTGAAA-ATTTTATTTAA
1 ATTAAACTATTTGAAAGATTTTATTTAA
17582340 AACACCGGGC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.52
Consensus pattern (31 bp):
ATTAAACTATTTGAAAGATTTTATTTAAGTT
Found at i:17583683 original size:16 final size:16
Alignment explanation
Indices: 17583657--17583710 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
17583647 TTTGGTTCGC
*
17583657 TGTATTGGAATAGAGG
1 TGTAATGGAATAGAGG
*
17583673 CGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
*
17583689 TGTAATGAAATAGAGG
1 TGTAATGGAATAGAGG
17583705 TGTAAT
1 TGTAAT
17583711 AGCAAATCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.37, C:0.02, G:0.33, T:0.28
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:17583740 original size:45 final size:44
Alignment explanation
Indices: 17583689--17583798 Score: 113
Period size: 45 Copynumber: 2.6 Consensus size: 44
17583679 GGAATAGAGG
17583689 TGTAATGAAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATG-AATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
* * * ***
17583734 TGTAATGGAATATAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAAT-GAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
17583778 TG----GAATAGAGGTGTAATAGCA
1 TGTAATGAATAGAGGTGTAATAGCA
17583799 TAATGGAAAC
Statistics
Matches: 54, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
39 15 0.28
44 18 0.33
45 20 0.37
46 1 0.02
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
Found at i:17583961 original size:16 final size:16
Alignment explanation
Indices: 17583924--17583965 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
17583914 TTAATCATAT
*
17583924 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
17583940 TT-AAATATATTATAA
1 TTAAAATATATTATAA
17583955 TTAAAATATAT
1 TTAAAATATAT
17583966 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:17583972 original size:14 final size:15
Alignment explanation
Indices: 17583933--17583974 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
17583923 TTTAAACATA
*
17583933 ATTATTATTAAATAT
1 ATTATAATTAAATAT
17583948 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
17583962 A-TATAATTTAATA
1 ATTATAATTAAATA
17583975 AAATTCTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:17584073 original size:120 final size:121
Alignment explanation
Indices: 17583922--17584219 Score: 494
Period size: 120 Copynumber: 2.5 Consensus size: 121
17583912 ATTTAATCAT
* *
17583922 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAGTA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* *
17583987 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGA-AA
*
17584044 A-TT-AACATAATTATTATTAAATTTATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
17584107 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
* * *
17584163 ATTTGAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
17584220 TAAAATAATT
Statistics
Matches: 166, Mismatches: 8, Indels: 6
0.92 0.04 0.03
Matches are distributed among these distances:
119 3 0.02
120 158 0.95
121 4 0.02
122 1 0.01
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (121 bp):
ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
Found at i:17584157 original size:61 final size:61
Alignment explanation
Indices: 17583972--17584158 Score: 190
Period size: 61 Copynumber: 3.1 Consensus size: 61
17583962 ATATAATTTA
*
17583972 ATAAAATTCTTAGTAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
1 ATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
* * * * * * * * *
17584033 GTAAAA-T-AT-A-AATTAACATAATTATTAT-TAAATTTA-TTATAATTAAAATATATAAT-TT
1 ATAAAATTCTTAATAATT-A-AT-ATTCTTATATGAATTTACTCA-AATCATAATATATGATACT
17584091 AATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
1 -ATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
17584153 ATAAAA
1 ATAAAA
17584159 GAAAATTTGA
Statistics
Matches: 95, Mismatches: 19, Indels: 24
0.69 0.14 0.17
Matches are distributed among these distances:
57 4 0.04
58 4 0.04
59 28 0.29
60 16 0.17
61 34 0.36
62 5 0.05
63 4 0.04
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.42
Consensus pattern (61 bp):
ATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
Found at i:17587663 original size:106 final size:106
Alignment explanation
Indices: 17587479--17587745 Score: 421
Period size: 106 Copynumber: 2.5 Consensus size: 106
17587469 AGAGCAAGTG
* * *
17587479 AAAGCAGCAACCATGTGAT-AACTTTTCAT-TTGTGTTTGGAAAGAAAGGGAGTACAAAAGTAGA
1 AAAGCAGCAACCATGTGATAAATTTTTCATGAT-TGTTTGGAAAGAAAGGAAGTACAAAAGTAGA
*
17587542 ACACTAAGCTGATTCAGAATATATGTTGGAATGAATCAAAAC
65 AAACTAAGCTGATTCAGAATATATGTTGGAATGAATCAAAAC
*
17587584 AAAGCAGCAACCATGTGATAAATTTTTCATGATTGTTTGGAAAGAAAGGTAGTACAAAAGTAGAA
1 AAAGCAGCAACCATGTGATAAATTTTTCATGATTGTTTGGAAAGAAAGGAAGTACAAAAGTAGAA
*
17587649 AACTAAGCTGATTCAGAATATATGTTGGAATGAATCAAAAT
66 AACTAAGCTGATTCAGAATATATGTTGGAATGAATCAAAAC
* ** *
17587690 AAAGTAGCAACCATGCAATAACTTTTTCATGATTGTTTGGAAAGAAAGGAAGTACA
1 AAAGCAGCAACCATGTGATAAATTTTTCATGATTGTTTGGAAAGAAAGGAAGTACA
17587746 TCCACAATTG
Statistics
Matches: 150, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
105 19 0.13
106 130 0.87
107 1 0.01
ACGTcount: A:0.42, C:0.11, G:0.20, T:0.27
Consensus pattern (106 bp):
AAAGCAGCAACCATGTGATAAATTTTTCATGATTGTTTGGAAAGAAAGGAAGTACAAAAGTAGAA
AACTAAGCTGATTCAGAATATATGTTGGAATGAATCAAAAC
Found at i:17591088 original size:31 final size:31
Alignment explanation
Indices: 17591050--17591110 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
17591040 AGCCCATTTT
17591050 TATTTTAAAAAT-TTTCAAAAATTAAAAAAAG
1 TATTTTAAAAATATTT-AAAAATTAAAAAAAG
*
17591081 TATTTTAAAAATATTTTAAAATTAAAAAAA
1 TATTTTAAAAATATTTAAAAATTAAAAAAA
17591111 AATTAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 25 0.89
32 3 0.11
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (31 bp):
TATTTTAAAAATATTTAAAAATTAAAAAAAG
Found at i:17591127 original size:31 final size:31
Alignment explanation
Indices: 17591067--17591132 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
17591057 AAAATTTTCA
* **
17591067 AAAATTAAAAAAAGTATTTTAAAAATATTTT
1 AAAATTAAAAAAAGAATTAAAAAAATATTTT
17591098 AAAATTAAAAAAA-AATTAAAAAAAGTATTTT
1 AAAATTAAAAAAAGAATTAAAAAAA-TATTTT
17591129 AAAA
1 AAAA
17591133 ATATTTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 8 0.26
31 23 0.74
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (31 bp):
AAAATTAAAAAAAGAATTAAAAAAATATTTT
Found at i:17591132 original size:12 final size:11
Alignment explanation
Indices: 17591117--17591184 Score: 50
Period size: 11 Copynumber: 6.2 Consensus size: 11
17591107 AAAAAATTAA
17591117 AAAAAGTATTTT
1 AAAAA-TATTTT
17591129 AAAAATATTTT
1 AAAAATATTTT
**
17591140 -AAAAT-TTAA
1 AAAAATATTTT
* *
17591149 AAAAAAAATTT
1 AAAAATATTTT
* *
17591160 AAAAAGTATGTA
1 AAAAA-TATTTT
17591172 AAAAATATTTT
1 AAAAATATTTT
17591183 AA
1 AA
17591185 CATTAAAAAA
Statistics
Matches: 41, Mismatches: 12, Indels: 7
0.68 0.20 0.12
Matches are distributed among these distances:
9 2 0.05
10 9 0.22
11 18 0.44
12 12 0.29
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.35
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:17591149 original size:43 final size:42
Alignment explanation
Indices: 17591066--17591195 Score: 199
Period size: 42 Copynumber: 3.1 Consensus size: 42
17591056 AAAAATTTTC
17591066 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAA
1 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAA
17591108 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTTAAAAA
1 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA-TT-AAAA
* * * *
17591152 AAAAATT-TAAAAAGTATGTAAAAAATATTTTAACATTAAAA
1 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAA
17591193 AAA
1 AAA
17591196 TATATTTATT
Statistics
Matches: 82, Mismatches: 4, Indels: 5
0.90 0.04 0.05
Matches are distributed among these distances:
41 7 0.09
42 38 0.46
43 26 0.32
44 11 0.13
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (42 bp):
AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAA
Found at i:17591158 original size:13 final size:13
Alignment explanation
Indices: 17591140--17591164 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17591130 AAAATATTTT
17591140 AAAATTTAAAAAA
1 AAAATTTAAAAAA
17591153 AAAATTTAAAAA
1 AAAATTTAAAAA
17591165 GTATGTAAAA
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAATTTAAAAAA
Found at i:17591174 original size:31 final size:32
Alignment explanation
Indices: 17591108--17591175 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 32
17591098 AAAATTAAAA
* * *
17591108 AAAAATTAAAAAAAGTATTTTAAAAATATTTT
1 AAAAATTAAAAAAAGAAATTTAAAAATATTGT
*
17591140 AAAATTTAAAAAAA-AAATTTAAAAAGTA-TGT
1 AAAAATTAAAAAAAGAAATTTAAAAA-TATTGT
17591171 AAAAA
1 AAAAA
17591176 ATATTTTAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
31 15 0.50
32 15 0.50
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (32 bp):
AAAAATTAAAAAAAGAAATTTAAAAATATTGT
Found at i:17594889 original size:91 final size:91
Alignment explanation
Indices: 17594780--17594992 Score: 372
Period size: 91 Copynumber: 2.3 Consensus size: 91
17594770 TTAAATATCT
17594780 ATTGTATAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAA
1 ATTGTATAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAA
* *
17594845 ATTATATTTAATATTAATTATTTTAA
66 ATTATATGTAATAATAATTATTTTAA
*
17594871 ATTGTATAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAA
1 ATTGTATAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAA
17594936 ATTATATGTAATAATAATTATTTTAA
66 ATTATATGTAATAATAATTATTTTAA
* * *
17594962 ATTATACAAATTCATATAAGATAATTTATTA
1 ATTGTATAAATTCATATAAGAAAATTTATTA
17594993 GTTGTAATTA
Statistics
Matches: 116, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
91 116 1.00
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (91 bp):
ATTGTATAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAA
ATTATATGTAATAATAATTATTTTAA
Found at i:17594912 original size:44 final size:45
Alignment explanation
Indices: 17594780--17594913 Score: 132
Period size: 44 Copynumber: 3.0 Consensus size: 45
17594770 TTAAATATCT
17594780 ATTGTATAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGA
1 ATTGTATAAATTCATATAAGAAAATTTATTATCAAGAATTTTA-GA
* * * * * **
17594826 AAT-TATATA-TCATTATTAA-ATTATATTTAATATTAATTATTTTA-A
1 ATTGTATAAATTCA-TA-TAAGA--AAATTTATTATCAAGAATTTTAGA
17594871 ATTGTATAAATTCATATAAGAAAATTTATTATCAAGAATTTTA
1 ATTGTATAAATTCATATAAGAAAATTTATTATCAAGAATTTTA
17594914 TGAAATTATA
Statistics
Matches: 67, Mismatches: 14, Indels: 16
0.69 0.14 0.16
Matches are distributed among these distances:
44 20 0.30
45 14 0.21
46 13 0.19
47 20 0.30
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.46
Consensus pattern (45 bp):
ATTGTATAAATTCATATAAGAAAATTTATTATCAAGAATTTTAGA
Found at i:17594961 original size:26 final size:28
Alignment explanation
Indices: 17594907--17594967 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
17594897 TATTATCAAG
* *
17594907 AATTTTATGAAATTATATATTATTATTA
1 AATTATATGAAATAATATATTATTATTA
*
17594935 AATTATATGTAATAATA-ATTATT-TTA
1 AATTATATGAAATAATATATTATTATTA
17594961 AATTATA
1 AATTATA
17594968 CAAATTCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
AATTATATGAAATAATATATTATTATTA
Found at i:17594967 original size:44 final size:43
Alignment explanation
Indices: 17594825--17594967 Score: 121
Period size: 44 Copynumber: 3.2 Consensus size: 43
17594815 GAATTTTATG
* *
17594825 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTT
1 AAATTATATATTATTATTAAATTATA-TTAATAATAATTATTTT
* ** * *
17594869 AAATTGTATAAATTCATATAAGAAAATT-TATT-ATCAAGAATT-TTATG
1 AAA-T-TATATATT-AT-T-ATTAAATTATATTAAT-AATAATTATT-TT
17594916 AAATTATATATTATTATTAAATTATATGTAATAATAATTATTTT
1 AAATTATATATTATTATTAAATTATAT-TAATAATAATTATTTT
17594960 AAATTATA
1 AAATTATA
17594968 CAAATTCATA
Statistics
Matches: 76, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
42 6 0.08
43 4 0.05
44 21 0.28
45 12 0.16
46 11 0.14
47 13 0.17
48 3 0.04
49 6 0.08
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.48
Consensus pattern (43 bp):
AAATTATATATTATTATTAAATTATATTAATAATAATTATTTT
Found at i:17595085 original size:59 final size:58
Alignment explanation
Indices: 17595019--17595297 Score: 155
Period size: 61 Copynumber: 4.7 Consensus size: 58
17595009 ATTTTATTAA
*
17595019 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATCTTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTT-AAATTATATTTTATAGT
* * **
17595078 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTA-TT-AA-TA-ATTTTATTA-
1 ATCATATATT-TTAATT-A--AAA-T-ATAT-TTAATATTAATTATTTAAATTATATTTTA-TAG
*
17595138 A
58 T
* * * * *
17595139 ATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTACAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTAAATTATATTTTATAGT
* * ** *
17595198 ATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTA-TT-AA-GA-ATTTTATTA-
1 ATCATATATT-TTAATT-A--AAA-T-ATAT-TTAATATTAATTATTTAAATTATATTTTA-TAG
*
17595258 A
58 T
* *
17595259 ATTATATATTTTAATTAAAATATATTTAATAATAATTAT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTAT
17595298 GTTTAAATAT
Statistics
Matches: 164, Mismatches: 33, Indels: 50
0.66 0.13 0.20
Matches are distributed among these distances:
54 20 0.12
55 8 0.05
56 4 0.02
57 6 0.04
58 3 0.02
59 27 0.16
60 16 0.10
61 31 0.19
62 6 0.04
63 8 0.05
64 4 0.02
65 10 0.06
66 21 0.13
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (58 bp):
ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTAAATTATATTTTATAGT
Found at i:17595132 original size:120 final size:120
Alignment explanation
Indices: 17595008--17595305 Score: 499
Period size: 120 Copynumber: 2.5 Consensus size: 120
17594998 AATTATTTTA
* * *
17595008 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATCTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATATTT
* * *
17595072 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAT
65 TACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAG
* *
17595128 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
17595193 ACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAG
17595248 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATG-TTAAAT
17595306 ATGATTAAAT
Statistics
Matches: 166, Mismatches: 10, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
120 159 0.96
121 7 0.04
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAG
Found at i:17595162 original size:18 final size:18
Alignment explanation
Indices: 17595116--17595163 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
17595106 TATAAGAATA
*
17595116 TTAATTATTA-ATA-ATT
1 TTAATTATAATATATATT
17595132 TT-ATTA-AATTATATATT
1 TTAATTATAA-TATATATT
17595149 TTAATTATAATATAT
1 TTAATTATAATATAT
17595164 TTAATAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
14 1 0.04
15 4 0.15
16 5 0.19
17 5 0.19
18 9 0.35
19 2 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTAATTATAATATATATT
Found at i:17595168 original size:15 final size:15
Alignment explanation
Indices: 17595133--17595184 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
17595123 TTAATAATTT
*
17595133 TATTAAATTAT-ATA
1 TATTTAATTATAATA
17595147 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
17595161 TATTTAATAATAAT-
1 TATTTAATTATAATA
17595175 TATGTTAATT
1 TAT-TTAATT
17595185 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:17595277 original size:18 final size:17
Alignment explanation
Indices: 17595249--17595283 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
17595239 ATTATTAAGA
*
17595249 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
17595266 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
17595284 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:17595553 original size:16 final size:16
Alignment explanation
Indices: 17595519--17595571 Score: 97
Period size: 16 Copynumber: 3.2 Consensus size: 16
17595509 GATTAGCTAT
17595519 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
17595536 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
17595552 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
17595568 TACA
1 TACA
17595572 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 24 0.67
17 12 0.33
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:17620724 original size:21 final size:21
Alignment explanation
Indices: 17620700--17620741 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
17620690 AGTTAGATGA
17620700 GATGGGACTGAGGAGTGTGCC
1 GATGGGACTGAGGAGTGTGCC
17620721 GATGGGACTGAGGAGTGTGCC
1 GATGGGACTGAGGAGTGTGCC
17620742 ATAGGAGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.14, G:0.48, T:0.19
Consensus pattern (21 bp):
GATGGGACTGAGGAGTGTGCC
Found at i:17621666 original size:25 final size:25
Alignment explanation
Indices: 17621632--17621686 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
17621622 CTGACAGGCC
17621632 GTACATATAGGAGGTAAACTACGTT
1 GTACATATAGGAGGTAAACTACGTT
17621657 GTACATATAGGAGGTAAACTACGTT
1 GTACATATAGGAGGTAAACTACGTT
17621682 GTACA
1 GTACA
17621687 AAAGGAACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (25 bp):
GTACATATAGGAGGTAAACTACGTT
Found at i:17623829 original size:32 final size:34
Alignment explanation
Indices: 17623793--17623864 Score: 98
Period size: 32 Copynumber: 2.2 Consensus size: 34
17623783 TTAAAAAAAG
17623793 ATTTTCACA-TTAATG-TTATTTACAATTTTTAA-
1 ATTTTCACAGTTAA-GATTATTTACAATTTTTAAT
*
17623825 ATTTT-ATAGTTAAGATTATTTACAATTTTTAAT
1 ATTTTCACAGTTAAGATTATTTACAATTTTTAAT
17623858 ATTTTCA
1 ATTTTCA
17623865 AATTCTTAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
31 3 0.09
32 26 0.74
33 5 0.14
34 1 0.03
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.54
Consensus pattern (34 bp):
ATTTTCACAGTTAAGATTATTTACAATTTTTAAT
Found at i:17631544 original size:69 final size:69
Alignment explanation
Indices: 17631459--17631598 Score: 208
Period size: 69 Copynumber: 2.0 Consensus size: 69
17631449 TTTGTTGGTT
*
17631459 TGTTCTGGAAATTGTTTTGATAGTCTGCTGGAAAATGTTATTAATTTGTTAGTGAGTAGAAGATG
1 TGTTCTGGAAATTGTTTTGATAGTCTGCTGGAAAATGTTATTAATTTGTTAGTCAGTAGAAGATG
17631524 AAAC
66 AAAC
* * * * * * *
17631528 TGTTCTGGCAGTTGTTTTGATTGTCTGCTGGAAATTGTTCTTGATTTGTTAGTCAGTAGAATATG
1 TGTTCTGGAAATTGTTTTGATAGTCTGCTGGAAAATGTTATTAATTTGTTAGTCAGTAGAAGATG
17631593 AAAC
66 AAAC
17631597 TG
1 TG
17631599 GAAATCAAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
69 63 1.00
ACGTcount: A:0.26, C:0.08, G:0.25, T:0.41
Consensus pattern (69 bp):
TGTTCTGGAAATTGTTTTGATAGTCTGCTGGAAAATGTTATTAATTTGTTAGTCAGTAGAAGATG
AAAC
Found at i:17635401 original size:47 final size:45
Alignment explanation
Indices: 17635350--17635517 Score: 141
Period size: 47 Copynumber: 3.6 Consensus size: 45
17635340 TATTTAATAT
17635350 TAATTATTTTAAATTGTATAAATTCATATAAGAAAATTTATTATCAA
1 TAATTATTTTAAATT-TATAAATTCATATAAGAAAATTTATTAT-AA
* * **
17635397 TAATT-TTATGAAA-TTATATATT-AT-T-ATTAAATTATATGTAATAA
1 TAATTATT-TTAAATTTATAAATTCATATAAGAAAATT-TAT-T-ATAA
* * *
17635441 TAATTATTTTAAATTATACAAATTCATATAAGATAATTTATTAGTTA
1 TAATTATTTTAAATT-TATAAATTCATATAAGAAAATTTATTA-TAA
17635488 TAATTATTTTAAATTTTATTAAA-TCATATA
1 TAATTATTTTAAA-TTTA-TAAATTCATATA
17635518 TTTTAATTAA
Statistics
Matches: 96, Mismatches: 12, Indels: 26
0.72 0.09 0.19
Matches are distributed among these distances:
42 6 0.06
43 4 0.04
44 14 0.15
45 12 0.12
46 10 0.10
47 36 0.38
48 9 0.09
49 5 0.05
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (45 bp):
TAATTATTTTAAATTTATAAATTCATATAAGAAAATTTATTATAA
Found at i:17635423 original size:91 final size:91
Alignment explanation
Indices: 17635276--17635483 Score: 326
Period size: 91 Copynumber: 2.3 Consensus size: 91
17635266 TTGATTTTAG
* *
17635276 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
* * *
17635341 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATAATAATTATTTTAAATTATA
* *
17635368 TAAATTCATATAAGAAAATTTATTATCAATAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
17635433 TGTAATAATAATTATTTTAAATTATA
66 TGTAATAATAATTATTTTAAATTATA
* *
17635459 CAAATTCATATAAGATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
17635484 GTTATAATTA
Statistics
Matches: 107, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
91 91 0.85
92 16 0.15
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TGTAATAATAATTATTTTAAATTATA
Found at i:17635443 original size:44 final size:43
Alignment explanation
Indices: 17635297--17635458 Score: 125
Period size: 44 Copynumber: 3.6 Consensus size: 43
17635287 AAGAACATTT
* * *
17635297 TATTATTAAGAATT-TTATGAAATTATATATCATTATTAAATTA
1 TATTAATAATAATTATT-TGAAATTATATATTATTATTAAATTA
* * * **
17635340 TATTTAATATTAATTATTTTAAATTGTATAAATTCATATAAGAAAATT-
1 TA-TTAATAATAATTATTTGAAA-T-TATATATT-AT-T-ATTAAATTA
17635388 TATT-ATCAATAATT-TTATGAAATTATATATTATTATTAAATTA
1 TATTAAT-AATAATTATT-TGAAATTATATATTATTATTAAATTA
*
17635431 TATGTAATAATAATTATTTTAAATTATA
1 TAT-TAATAATAATTATTTGAAATTATA
17635459 CAAATTCATA
Statistics
Matches: 92, Mismatches: 14, Indels: 25
0.70 0.11 0.19
Matches are distributed among these distances:
42 6 0.07
43 6 0.07
44 32 0.35
45 14 0.15
46 11 0.12
47 14 0.15
48 3 0.03
49 6 0.07
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (43 bp):
TATTAATAATAATTATTTGAAATTATATATTATTATTAAATTA
Found at i:17635452 original size:26 final size:28
Alignment explanation
Indices: 17635398--17635458 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
17635388 TATTATCAAT
* *
17635398 AATTTTATGAAATTATATATTATTATTA
1 AATTATATGAAATAATATATTATTATTA
*
17635426 AATTATATGTAATAATA-ATTATT-TTA
1 AATTATATGAAATAATATATTATTATTA
17635452 AATTATA
1 AATTATA
17635459 CAAATTCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
AATTATATGAAATAATATATTATTATTA
Found at i:17635654 original size:16 final size:16
Alignment explanation
Indices: 17635633--17635674 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
17635623 TTATTAAATT
*
17635633 ATATATTTTAATTATA
1 ATATATTTTAATAATA
17635649 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
17635664 AT-TATGTTTAA
1 ATATAT-TTTAA
17635675 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:17635659 original size:15 final size:15
Alignment explanation
Indices: 17635624--17635665 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
17635614 TTAAGAATTT
*
17635624 TATTAAATTAT-ATA
1 TATTTAATTATAATA
17635638 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
17635652 TATTTAATAATAAT
1 TATTTAATTATAAT
17635666 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:17635845 original size:39 final size:40
Alignment explanation
Indices: 17635802--17635905 Score: 111
Period size: 44 Copynumber: 2.5 Consensus size: 40
17635792 TTCCATTATG
*
17635802 CTATTACACCTCTATTCCATTCAACCAAATACAAGA-TTA
1 CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
* *** *
17635841 CTATTACGCCTCTATTCATTACATTCAACCAAACAGTTGATTTC
1 CTATTACACCTCTATTC----CATTCAACCAAACACAAGATTTA
17635885 CTATTACACCTCTATTCCATT
1 CTATTACACCTCTATTCCATT
17635906 ACACCTCTAT
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
39 16 0.30
40 4 0.08
43 15 0.28
44 18 0.34
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.36
Consensus pattern (40 bp):
CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
Found at i:17635908 original size:16 final size:16
Alignment explanation
Indices: 17635882--17635940 Score: 73
Period size: 16 Copynumber: 3.6 Consensus size: 16
17635872 AACAGTTGAT
17635882 TTCCTATTACACCTCTA
1 TTCC-ATTACACCTCTA
17635899 TTCCATTACACCTCTA
1 TTCCATTACACCTCTA
* *
17635915 TTCTATTACGCCTCTA
1 TTCCATTACACCTCTA
* *
17635931 ATCCAATACA
1 TTCCATTACA
17635941 GCGAACCAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
16 32 0.89
17 4 0.11
ACGTcount: A:0.27, C:0.34, G:0.02, T:0.37
Consensus pattern (16 bp):
TTCCATTACACCTCTA
Found at i:17644857 original size:19 final size:19
Alignment explanation
Indices: 17644807--17644861 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
17644797 TTTTCATTAA
17644807 TTTATTGATTAATTGACTATT
1 TTTATTG-TT-ATTGACTATT
*
17644828 TTTATTTTTATT-ACTATT
1 TTTATTGTTATTGACTATT
17644846 TATTATTGTTATTGAC
1 T-TTATTGTTATTGAC
17644862 ATTATTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
18 7 0.23
19 13 0.43
20 4 0.13
21 6 0.20
ACGTcount: A:0.25, C:0.05, G:0.07, T:0.62
Consensus pattern (19 bp):
TTTATTGTTATTGACTATT
Done.