Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 103 of 226
Found at i:35613480 original size:15 final size:15
Alignment explanation
Indices: 35613460--35613520 Score: 54
Period size: 15 Copynumber: 4.0 Consensus size: 15
35613450 TCTTTTTCAA
*
35613460 TCTCACTTTATTTTT
1 TCTCACTTTCTTTTT
*
35613475 TCTCACTCTT-TTTCT
1 TCTCACT-TTCTTTTT
35613490 TCTTCGA-TTTCTTTTT
1 TC-TC-ACTTTCTTTTT
*
35613506 TCGCACTTTCTTTTT
1 TCTCACTTTCTTTTT
35613521 CTTTTTTGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 1 0.03
15 25 0.66
16 11 0.29
17 1 0.03
ACGTcount: A:0.08, C:0.25, G:0.03, T:0.64
Consensus pattern (15 bp):
TCTCACTTTCTTTTT
Found at i:35613505 original size:31 final size:32
Alignment explanation
Indices: 35613470--35613542 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 32
35613460 TCTCACTTTA
*
35613470 TTTTTTCTCAC-TCTTTTTCTTCTTCGATTTC
1 TTTTTTCTCACTTCTTTTTCTTCTTCGATTAC
* * *
35613501 TTTTTTCGCACTTTCTTTTTCTTTTTTGATTAC
1 TTTTTTCTCAC-TTCTTTTTCTTCTTCGATTAC
35613534 TTTTCTTCT
1 TTTT-TTCT
35613543 TTCAAGCTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
31 10 0.29
33 21 0.62
34 3 0.09
ACGTcount: A:0.07, C:0.22, G:0.04, T:0.67
Consensus pattern (32 bp):
TTTTTTCTCACTTCTTTTTCTTCTTCGATTAC
Found at i:35614994 original size:26 final size:26
Alignment explanation
Indices: 35614934--35615027 Score: 107
Period size: 26 Copynumber: 3.6 Consensus size: 26
35614924 CACAGCAAAA
* *
35614934 CTGCCAATAATAGTATCGCAACGAAG
1 CTGCCAGTAATAGTATCGCAGCGAAG
*
35614960 CTGCCAGTAATAATATCGCAGCGAAG
1 CTGCCAGTAATAGTATCGCAGCGAAG
* * * * *
35614986 CTGCTAGTATTAGTATTGTAGCAAAG
1 CTGCCAGTAATAGTATCGCAGCGAAG
*
35615012 CTGCCAGTAACAGTAT
1 CTGCCAGTAATAGTAT
35615028 ATGTGGCAAA
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.24
Consensus pattern (26 bp):
CTGCCAGTAATAGTATCGCAGCGAAG
Found at i:35615050 original size:26 final size:27
Alignment explanation
Indices: 35614997--35615054 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
35614987 TGCTAGTATT
**
35614997 AGTAT-TGTAGCAAAGCTGCCAGTAAC
1 AGTATATGTAGCAAAGCCACCAGTAAC
*
35615023 AGTATATGTGGCAAAGCCACCAGT-AC
1 AGTATATGTAGCAAAGCCACCAGTAAC
35615049 AGTATA
1 AGTATA
35615055 CTTCCTCCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 13 0.46
27 15 0.54
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.22
Consensus pattern (27 bp):
AGTATATGTAGCAAAGCCACCAGTAAC
Found at i:35624405 original size:26 final size:26
Alignment explanation
Indices: 35624376--35624456 Score: 99
Period size: 26 Copynumber: 3.1 Consensus size: 26
35624366 AACACACCAA
*
35624376 TATCGCAACAAAGCTTCCAGTAATAG
1 TATCGCAACAAAGCTGCCAGTAATAG
* *
35624402 TATCGCAGCAAAGCTGCCAGTATTAG
1 TATCGCAACAAAGCTGCCAGTAATAG
* * * *
35624428 TATTGCAACAATGCTGGCAGTAACAG
1 TATCGCAACAAAGCTGCCAGTAATAG
35624454 TAT
1 TAT
35624457 ATGTAGTAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.25
Consensus pattern (26 bp):
TATCGCAACAAAGCTGCCAGTAATAG
Found at i:35628313 original size:20 final size:20
Alignment explanation
Indices: 35628290--35628328 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
35628280 TACTTTCTTC
35628290 TTTACTTACTCACTTACTTG
1 TTTACTTACTCACTTACTTG
*
35628310 TTTACTTACTCGCTTACTT
1 TTTACTTACTCACTTACTT
35628329 AAATAACTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.26, G:0.05, T:0.51
Consensus pattern (20 bp):
TTTACTTACTCACTTACTTG
Found at i:35628604 original size:49 final size:49
Alignment explanation
Indices: 35628530--35628660 Score: 138
Period size: 49 Copynumber: 2.6 Consensus size: 49
35628520 GATAATAACA
* * * * * * *
35628530 TGCCAAAGTCATATCCTAGACATGGTCTTACATTGGATGTTTCCTGTAT-
1 TGCCAATGCCATATCCCAAACATGGTCTTACATGGGATG-TTCATATATG
*
35628579 TGCCAATGCCATATCCCAAATATGGTCTTACATGGGATGTTCATATATCGG
1 TGCCAATGCCATATCCCAAACATGGTCTTACATGGGATGTTCATATAT--G
* *
35628630 TGCCAATGCCATGTCCCAGACATGGTCTTAC
1 TGCCAATGCCATATCCCAAACATGGTCTTAC
35628661 GGGGAACCTC
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
48 7 0.10
49 33 0.49
51 28 0.41
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (49 bp):
TGCCAATGCCATATCCCAAACATGGTCTTACATGGGATGTTCATATATG
Found at i:35628655 original size:51 final size:50
Alignment explanation
Indices: 35628547--35628716 Score: 150
Period size: 50 Copynumber: 3.4 Consensus size: 50
35628537 GTCATATCCT
* * *
35628547 AGACATGGTCTTACATTGGATGTTTCCTGTAT---TGCCAATGCCATATCCC
1 AGACATGGTCTTACATGGGATG-TT-CTATATCGGTGCCAATGCCATGTCCC
* *
35628596 AAATATGGTCTTACATGGGATGTTCATATATCGGTGCCAATGCCATGTCCC
1 AGACATGGTCTTACATGGGATGTTC-TATATCGGTGCCAATGCCATGTCCC
* *** * * **
35628647 AGACATGGTCTTAC-GGGGAACCTCTCATCTCGGTGCCAAAGCCATGTCGT
1 AGACATGGTCTTACATGGGATGTTCT-ATATCGGTGCCAATGCCATGTCCC
*
35628697 AGACATGGTCTTACGTGGGA
1 AGACATGGTCTTACATGGGA
35628717 CCTCTCATAA
Statistics
Matches: 99, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
47 1 0.01
48 6 0.06
49 20 0.20
50 40 0.40
51 32 0.32
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (50 bp):
AGACATGGTCTTACATGGGATGTTCTATATCGGTGCCAATGCCATGTCCC
Found at i:35628692 original size:50 final size:50
Alignment explanation
Indices: 35628626--35628724 Score: 155
Period size: 50 Copynumber: 2.0 Consensus size: 50
35628616 TGTTCATATA
*
35628626 TCGGTGCCAATGCCATGTCCCAGACATGGTCTTACG-GGGAACCTCTCATC
1 TCGGTGCCAAAGCCATGTCCCAGACATGGTCTTACGTGGG-ACCTCTCATC
**
35628676 TCGGTGCCAAAGCCATGTCGTAGACATGGTCTTACGTGGGACCTCTCAT
1 TCGGTGCCAAAGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCAT
35628725 AACCTCAATA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
50 42 0.93
51 3 0.07
ACGTcount: A:0.20, C:0.29, G:0.25, T:0.25
Consensus pattern (50 bp):
TCGGTGCCAAAGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATC
Found at i:35640816 original size:39 final size:39
Alignment explanation
Indices: 35640773--35640871 Score: 146
Period size: 39 Copynumber: 2.5 Consensus size: 39
35640763 CGGCTCTGCA
* *
35640773 CCTAGCAGGCTTCGTGTCGGTGACATATCGAGCTTTTAG
1 CCTAGCAGGCTTCATGTCGATGACATATCGAGCTTTTAG
* *
35640812 CCTAGCAGGCTTCATTTCGATGACTTATCGAGCTTTTAG
1 CCTAGCAGGCTTCATGTCGATGACATATCGAGCTTTTAG
35640851 CCTAGTC-GGCTTCATGTCGAT
1 CCTAG-CAGGCTTCATGTCGAT
35640872 CTTTATCGAG
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
39 53 0.98
40 1 0.02
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.33
Consensus pattern (39 bp):
CCTAGCAGGCTTCATGTCGATGACATATCGAGCTTTTAG
Found at i:35655564 original size:15 final size:15
Alignment explanation
Indices: 35655535--35655564 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
35655525 GCTTAGTGAC
35655535 TTTTGACTTGATTTT
1 TTTTGACTTGATTTT
35655550 TTTTG-CTTGATTTT
1 TTTTGACTTGATTTT
35655564 T
1 T
35655565 AAGCAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.10, C:0.07, G:0.13, T:0.70
Consensus pattern (15 bp):
TTTTGACTTGATTTT
Found at i:35658341 original size:25 final size:25
Alignment explanation
Indices: 35658302--35658395 Score: 89
Period size: 25 Copynumber: 3.8 Consensus size: 25
35658292 TCATGTACAT
* * * *
35658302 GTATGCTTATACGAGATGTGAATCG
1 GTATGCTCACACGAGCTGTAAATCG
* * *
35658327 GTATGCTCACTCGAGCTGCAGATCG
1 GTATGCTCACACGAGCTGTAAATCG
* * *
35658352 ATATGCTCTCACAAGCTGTAAATCG
1 GTATGCTCACACGAGCTGTAAATCG
*
35658377 GTATGCTCATACGAGCTGT
1 GTATGCTCACACGAGCTGT
35658396 GGGTTGGAAC
Statistics
Matches: 52, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
25 52 1.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (25 bp):
GTATGCTCACACGAGCTGTAAATCG
Found at i:35661777 original size:27 final size:27
Alignment explanation
Indices: 35661741--35661806 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
35661731 CAGCATAGCT
*
35661741 ACCAGT-ACAGT-ATATGTGGCAAAGTC
1 ACCAGTAACAGTAAT-TGTGGCAAAGCC
*
35661767 ACCAGTAACAGTAATTGTTGCAAAGCC
1 ACCAGTAACAGTAATTGTGGCAAAGCC
*
35661794 ACCAGAAACAGTA
1 ACCAGTAACAGTA
35661807 CTTCCTCTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
26 6 0.17
27 27 0.77
28 2 0.06
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.20
Consensus pattern (27 bp):
ACCAGTAACAGTAATTGTGGCAAAGCC
Found at i:35661970 original size:27 final size:27
Alignment explanation
Indices: 35661940--35662016 Score: 127
Period size: 27 Copynumber: 2.9 Consensus size: 27
35661930 CCTTAACGGA
*
35661940 GGTATTATGGTAATTATACCCATCAAG
1 GGTATTATGGTAATTTTACCCATCAAG
* *
35661967 GGTATTTTGGTAATTTTACCCATCGAG
1 GGTATTATGGTAATTTTACCCATCAAG
35661994 GGTATTATGGTAATTTTACCCAT
1 GGTATTATGGTAATTTTACCCAT
35662017 TGAAGGTATT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.39
Consensus pattern (27 bp):
GGTATTATGGTAATTTTACCCATCAAG
Found at i:35662032 original size:27 final size:27
Alignment explanation
Indices: 35661939--35662026 Score: 115
Period size: 27 Copynumber: 3.3 Consensus size: 27
35661929 ACCTTAACGG
* *
35661939 AGGTATTATGGTAATTATACCCA-TCA
1 AGGTATTATGGTAATTTTACCCATTGA
* *
35661965 AGGGTATTTTGGTAATTTTACCCATCGA
1 A-GGTATTATGGTAATTTTACCCATTGA
*
35661993 GGGTATTATGGTAATTTTACCCATTGA
1 AGGTATTATGGTAATTTTACCCATTGA
35662020 AGGTATT
1 AGGTATT
35662027 TCGGTATAGT
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
26 1 0.02
27 50 0.96
28 1 0.02
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.39
Consensus pattern (27 bp):
AGGTATTATGGTAATTTTACCCATTGA
Found at i:35668508 original size:13 final size:13
Alignment explanation
Indices: 35668490--35668516 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
35668480 TGCCTAAACA
35668490 CATATTCACCAAC
1 CATATTCACCAAC
35668503 CATATTCACCAAC
1 CATATTCACCAAC
35668516 C
1 C
35668517 GTGTTTGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.41, G:0.00, T:0.22
Consensus pattern (13 bp):
CATATTCACCAAC
Found at i:35669394 original size:29 final size:30
Alignment explanation
Indices: 35669335--35669392 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
35669325 TCCGAGCCTT
*
35669335 GGGGCAAAAATGTAATTATGCAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
35669365 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
35669393 AGAGTCGATG
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:0.41, C:0.05, G:0.24, T:0.29
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:35669805 original size:50 final size:50
Alignment explanation
Indices: 35669730--35669922 Score: 314
Period size: 50 Copynumber: 3.8 Consensus size: 50
35669720 ATTTGGGTAA
35669730 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
35669780 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
35669830 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
35669880 AGAACATCCCATGTAAGACCATGTGTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
35669923 TGTTATTATC
Statistics
Matches: 132, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
50 99 0.75
51 33 0.25
ACGTcount: A:0.26, C:0.22, G:0.31, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:35676879 original size:29 final size:30
Alignment explanation
Indices: 35676820--35676877 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
35676810 TCCGATCCTT
*
35676820 GGGGCAAAAATGTAATTATGCAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
35676850 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
35676878 AGAGTCGAGG
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:0.41, C:0.05, G:0.24, T:0.29
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:35677293 original size:50 final size:50
Alignment explanation
Indices: 35677215--35677450 Score: 364
Period size: 50 Copynumber: 4.7 Consensus size: 50
35677205 ATTTGGGTAA
35677215 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
* *
35677265 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
* *
35677315 AGAGGTCTCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
* * * *
35677365 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
** *
35677415 AGAACATCCCATGTAAGACCATGTGTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
35677451 TTTGTCATGT
Statistics
Matches: 170, Mismatches: 15, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
50 142 0.84
51 28 0.16
ACGTcount: A:0.27, C:0.22, G:0.31, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
Found at i:35679165 original size:25 final size:25
Alignment explanation
Indices: 35679070--35679157 Score: 176
Period size: 25 Copynumber: 3.5 Consensus size: 25
35679060 CACTTTGTGA
35679070 ATCGGTATGCTCACTCGAGCTGCAG
1 ATCGGTATGCTCACTCGAGCTGCAG
35679095 ATCGGTATGCTCACTCGAGCTGCAG
1 ATCGGTATGCTCACTCGAGCTGCAG
35679120 ATCGGTATGCTCACTCGAGCTGCAG
1 ATCGGTATGCTCACTCGAGCTGCAG
35679145 ATCGGTATGCTCA
1 ATCGGTATGCTCA
35679158 TATGAGCTAT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 63 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.25
Consensus pattern (25 bp):
ATCGGTATGCTCACTCGAGCTGCAG
Found at i:35679179 original size:50 final size:50
Alignment explanation
Indices: 35679069--35679180 Score: 163
Period size: 50 Copynumber: 2.2 Consensus size: 50
35679059 ACACTTTGTG
*
35679069 AATCGGTATGCTCACTCGAGCTGCAGATCGGTATGCTCACTCGAGCTGCA
1 AATCGGTATGCTCACTCGAGCTGCAGATCGGTATGCTCACTCGAGCTACA
* * *
35679119 GATCGGTATGCTCACTCGAGCTGCAGATCGGTATGCTCA-TATGAGCTATA
1 AATCGGTATGCTCACTCGAGCTGCAGATCGGTATGCTCACT-CGAGCTACA
*
35679169 AATCGATATGCT
1 AATCGGTATGCT
35679181 AATACGAGCT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
49 1 0.02
50 54 0.98
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.27
Consensus pattern (50 bp):
AATCGGTATGCTCACTCGAGCTGCAGATCGGTATGCTCACTCGAGCTACA
Found at i:35680632 original size:20 final size:20
Alignment explanation
Indices: 35680607--35680645 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
35680597 TACTTTCTTC
35680607 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
35680627 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
35680646 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:35680989 original size:50 final size:50
Alignment explanation
Indices: 35680919--35681041 Score: 138
Period size: 50 Copynumber: 2.5 Consensus size: 50
35680909 TCCCAGATAA
* ** * ***
35680919 GGTCTTACATGGGAGTTCTCATATTGGTGCCCGTGCCATGTCCCAAACAT
1 GGTCTTACAGGGGACCTCTCATATCGGTGCCAACGCCATGTCCCAAACAT
* * * *
35680969 GGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGATAT
1 GGTCTTACAGGGGACCTCTCATATCGGTGCCAACGCCATGTCCCAAACAT
*
35681019 GGTCTTACATGGGACCTCTCATA
1 GGTCTTACAGGGGACCTCTCATA
35681042 ACCTCAATAA
Statistics
Matches: 59, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
50 59 1.00
ACGTcount: A:0.20, C:0.28, G:0.24, T:0.28
Consensus pattern (50 bp):
GGTCTTACAGGGGACCTCTCATATCGGTGCCAACGCCATGTCCCAAACAT
Found at i:35683707 original size:11 final size:11
Alignment explanation
Indices: 35683691--35683721 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
35683681 CCAAGACCCT
35683691 AAATCATGCCC
1 AAATCATGCCC
35683702 AAATCATGCCC
1 AAATCATGCCC
*
35683713 AAAACATGC
1 AAATCATGC
35683722 ATAATGAGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.42, C:0.32, G:0.10, T:0.16
Consensus pattern (11 bp):
AAATCATGCCC
Found at i:35698546 original size:16 final size:16
Alignment explanation
Indices: 35698525--35698575 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
35698515 TGAATTACTA
35698525 ATTACAACTCTATTTC
1 ATTACAACTCTATTTC
* *
35698541 ATTACAGCTCTATTCC
1 ATTACAACTCTATTTC
*
35698557 ATTACAACCCTATTTC
1 ATTACAACTCTATTTC
35698573 ATT
1 ATT
35698576 CCAATTAACC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.29, C:0.27, G:0.02, T:0.41
Consensus pattern (16 bp):
ATTACAACTCTATTTC
Found at i:35699564 original size:34 final size:33
Alignment explanation
Indices: 35699484--35699600 Score: 108
Period size: 34 Copynumber: 3.5 Consensus size: 33
35699474 CAAATATCAT
* * * * *
35699484 ATCAGAATGTCACATTACCAGAAACATTTATCAA
1 ATCAGAATGTCATATT-TCATAAACATATACCAA
35699518 ATCAGAATGTCATATTTCAATAAACATATACCAA
1 ATCAGAATGTCATATTTC-ATAAACATATACCAA
* * * *
35699552 GTCAGAATGTCATATTTTCGTAAACATATATCAT
1 ATCAGAATGTCATA-TTTCATAAACATATACCAA
* *
35699586 ATAAGAATGCCATAT
1 ATCAGAATGTCATAT
35699601 CATATCAGAA
Statistics
Matches: 69, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
33 2 0.03
34 63 0.91
35 4 0.06
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.31
Consensus pattern (33 bp):
ATCAGAATGTCATATTTCATAAACATATACCAA
Found at i:35699805 original size:46 final size:46
Alignment explanation
Indices: 35699736--35699828 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
35699726 GCTGCCAAAC
35699736 AAATATTGAAGTTTAACCGCCAGTATTGTAGTAATACTACTAGAAA
1 AAATATTGAAGTTTAACCGCCAGTATTGTAGTAATACTACTAGAAA
*
35699782 AAATATTGAAGTTTAACCTCCAGTATTGTAGTAATACTACTAGAAA
1 AAATATTGAAGTTTAACCGCCAGTATTGTAGTAATACTACTAGAAA
35699828 A
1 A
35699829 CACTTTCTCC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (46 bp):
AAATATTGAAGTTTAACCGCCAGTATTGTAGTAATACTACTAGAAA
Found at i:35700941 original size:17 final size:17
Alignment explanation
Indices: 35700907--35700941 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
35700897 AGAACTCAAT
*
35700907 AGAGAAAAAGAAAGAAA
1 AGAGAAAAAGAAAAAAA
*
35700924 AGAGGAAAAGAAAAAAA
1 AGAGAAAAAGAAAAAAA
35700941 A
1 A
35700942 TGAAAGTGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (17 bp):
AGAGAAAAAGAAAAAAA
Found at i:35703055 original size:28 final size:28
Alignment explanation
Indices: 35703052--35703280 Score: 343
Period size: 28 Copynumber: 8.2 Consensus size: 28
35703042 CTATTCAGTA
*
35703052 ACAGT-ACAGTGTGGGCCTTAGCCCAAT
1 ACAGTAACAATGTGGGCCTTAGCCCAAT
* *
35703079 ACAGTAATAATGAGGGCCTTAGCCCAAT
1 ACAGTAACAATGTGGGCCTTAGCCCAAT
*
35703107 ACAGTAACAATGTGGGCCTTAGCCGAAT
1 ACAGTAACAATGTGGGCCTTAGCCCAAT
35703135 ACAGTAACAATGTGGGCCTTAGCCCAAT
1 ACAGTAACAATGTGGGCCTTAGCCCAAT
* *
35703163 ATAGTAATAATGTGGGCCTTAGCCCAAT
1 ACAGTAACAATGTGGGCCTTAGCCCAAT
* * *
35703191 TCAGTAACAATGTCGGCCTTAGCTCAAT
1 ACAGTAACAATGTGGGCCTTAGCCCAAT
*
35703219 ACAGTAACAATGTGGGCCTTAACCCAAT
1 ACAGTAACAATGTGGGCCTTAGCCCAAT
* *
35703247 GCAGTAACAATGTGGGCCTTAGCCCTAT
1 ACAGTAACAATGTGGGCCTTAGCCCAAT
35703275 ACAGTA
1 ACAGTA
35703281 TCGATACAGT
Statistics
Matches: 179, Mismatches: 22, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
27 5 0.03
28 174 0.97
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (28 bp):
ACAGTAACAATGTGGGCCTTAGCCCAAT
Found at i:35703067 original size:33 final size:34
Alignment explanation
Indices: 35703019--35703115 Score: 91
Period size: 33 Copynumber: 3.1 Consensus size: 34
35703009 ATACAACAAG
* * *
35703019 CAGTGACAGTTTGGGCCTAAGCCCTATTCAGTAA
1 CAGTGACAGTGTGGGCCTAAGCCCAATACAGTAA
*
35703053 CAGT-ACAGTGTGGGCCTTAGCCCAATACAGT-A
1 CAGTGACAGTGTGGGCCTAAGCCCAATACAGTAA
* *
35703085 -A-T-A-A-TGAGGGCCTTAGCCCAATACAGTAA
1 CAGTGACAGTGTGGGCCTAAGCCCAATACAGTAA
35703114 CA
1 CA
35703116 ATGTGGGCCT
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
28 22 0.39
29 2 0.04
30 3 0.05
31 1 0.02
32 1 0.02
33 23 0.41
34 4 0.07
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.23
Consensus pattern (34 bp):
CAGTGACAGTGTGGGCCTAAGCCCAATACAGTAA
Found at i:35703628 original size:27 final size:27
Alignment explanation
Indices: 35703597--35703651 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
35703587 AGCAAATCAG
35703597 TCATAACATAAGGCCATAATAGTCATT
1 TCATAACATAAGGCCATAATAGTCATT
* * * **
35703624 TCATATCCTAGGGGTATAATAGTCATT
1 TCATAACATAAGGCCATAATAGTCATT
35703651 T
1 T
35703652 TACCCTATAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Consensus pattern (27 bp):
TCATAACATAAGGCCATAATAGTCATT
Found at i:35703662 original size:27 final size:26
Alignment explanation
Indices: 35703645--35704001 Score: 311
Period size: 27 Copynumber: 13.3 Consensus size: 26
35703635 GGGTATAATA
* *
35703645 GTCATTTTACCCTATAGGGATATTTTG
1 GTCATTTTACCCTATAGGGGTA-ATTG
*
35703672 GTCATTTTACCCTATGGGGGTAATTCG
1 GTCATTTTACCCTATAGGGGTAATT-G
* *
35703699 GTAATTTTACCCTATAGGGGTAATTTA
1 GTCATTTTACCCTATAGGGGTAA-TTG
*
35703726 GTCATTTTACCCTATCGGGGTAATTCG
1 GTCATTTTACCCTATAGGGGTAATT-G
35703753 GTCATTTTACCCTATA-GGGTAATTCG
1 GTCATTTTACCCTATAGGGGTAATT-G
* * *
35703779 ATCATTTTACCCTGTGGGGGTAATTCG
1 GTCATTTTACCCTATAGGGGTAATT-G
* * * *
35703806 CTCATTTTACCTTGTGGGGGTAATTCG
1 GTCATTTTACCCTATAGGGGTAATT-G
* * * *
35703833 ATCATTTTACCGTGTGGGGGTAATTCG
1 GTCATTTTACCCTATAGGGGTAATT-G
* * *
35703860 ATCATTTTACCCTGTGGGGGTAATTCG
1 GTCATTTTACCCTATAGGGGTAATT-G
* * *
35703887 GTCATTTTACACTGTGGGGGTAATTCG
1 GTCATTTTACCCTATAGGGGTAATT-G
* *
35703914 GTCATTTTACCCTGTGGGGGTAATTCG
1 GTCATTTTACCCTATAGGGGTAATT-G
* * * *
35703941 CTCATTTTAACCTATGGGGGTAACTCG
1 GTCATTTTACCCTATAGGGGTAA-TTG
* *
35703968 GTCATTTTACCCTGTGGGGGTAATTCG
1 GTCATTTTACCCTATAGGGGTAATT-G
35703995 GTCATTT
1 GTCATTT
35704002 ATTGACCTCT
Statistics
Matches: 295, Mismatches: 29, Indels: 12
0.88 0.09 0.04
Matches are distributed among these distances:
26 28 0.09
27 264 0.89
28 3 0.01
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (26 bp):
GTCATTTTACCCTATAGGGGTAATTG
Found at i:35703767 original size:81 final size:81
Alignment explanation
Indices: 35703643--35704001 Score: 452
Period size: 81 Copynumber: 4.4 Consensus size: 81
35703633 AGGGGTATAA
* * * * * * *
35703643 TAGTCATTTTACCCTATAGGGATATTTTGGTCATTTTACCCTATGGGGGTAATTCGGTAATTTTA
1 TAGTCATTTTACCCTGTGGGGGTAATTCGGTCATTTTACCCTATGGGGGTAATTCGATCATTTTA
*
35703708 CCCTATAGGGGTAATT
66 CCCTATGGGGGTAATT
* * *
35703724 TAGTCATTTTACCCTATCGGGGTAATTCGGTCATTTTACCCTAT-AGGGTAATTCGATCATTTTA
1 TAGTCATTTTACCCTGTGGGGGTAATTCGGTCATTTTACCCTATGGGGGTAATTCGATCATTTTA
*
35703788 CCCTGTGGGGGTAA-T
66 CCCTATGGGGGTAATT
* * * * *
35703803 TCGCTCATTTTACCTTGTGGGGGTAATTCGATCATTTTACCGTGTGGGGGTAATTCGATCATTTT
1 TAG-TCATTTTACCCTGTGGGGGTAATTCGGTCATTTTACCCTATGGGGGTAATTCGATCATTTT
*
35703868 ACCCTGTGGGGGTAATT
65 ACCCTATGGGGGTAATT
** * * *
35703885 CGGTCATTTTACACTGTGGGGGTAATTCGGTCATTTTACCCTGTGGGGGTAATTCGCTCATTTTA
1 TAGTCATTTTACCCTGTGGGGGTAATTCGGTCATTTTACCCTATGGGGGTAATTCGATCATTTTA
* *
35703950 ACCTATGGGGGTAACT
66 CCCTATGGGGGTAATT
**
35703966 CGGTCATTTTACCCTGTGGGGGTAATTCGGTCATTT
1 TAGTCATTTTACCCTGTGGGGGTAATTCGGTCATTT
35704002 ATTGACCTCT
Statistics
Matches: 247, Mismatches: 28, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
79 3 0.01
80 64 0.26
81 178 0.72
82 2 0.01
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (81 bp):
TAGTCATTTTACCCTGTGGGGGTAATTCGGTCATTTTACCCTATGGGGGTAATTCGATCATTTTA
CCCTATGGGGGTAATT
Found at i:35703981 original size:54 final size:54
Alignment explanation
Indices: 35703645--35704001 Score: 441
Period size: 54 Copynumber: 6.6 Consensus size: 54
35703635 GGGTATAATA
* * * * * *
35703645 GTCATTTTACCCTATAGGGATATTTTGGTCATTTTACCCTATGGGGGTAATTCG
1 GTCATTTTACCCTGTGGGGGTAATTCGGTCATTTTAACCTATGGGGGTAATTCG
* * * ** * *
35703699 GTAATTTTACCCTATAGGGGTAATTTAGTCATTTTACCCTATCGGGGTAATTCG
1 GTCATTTTACCCTGTGGGGGTAATTCGGTCATTTTAACCTATGGGGGTAATTCG
* * * * *
35703753 GTCATTTTACCCTAT-AGGGTAATTCGATCATTTTACCCTGTGGGGGTAATTCG
1 GTCATTTTACCCTGTGGGGGTAATTCGGTCATTTTAACCTATGGGGGTAATTCG
* * * *
35703806 CTCATTTTACCTTGTGGGGGTAATTCGATCATTTT-ACCGTGTGGGGGTAATTCG
1 GTCATTTTACCCTGTGGGGGTAATTCGGTCATTTTAACC-TATGGGGGTAATTCG
* *
35703860 ATCATTTTACCCTGTGGGGGTAATTCGGTCATTTT-ACACTGTGGGGGTAATTCG
1 GTCATTTTACCCTGTGGGGGTAATTCGGTCATTTTAAC-CTATGGGGGTAATTCG
* *
35703914 GTCATTTTACCCTGTGGGGGTAATTCGCTCATTTTAACCTATGGGGGTAACTCG
1 GTCATTTTACCCTGTGGGGGTAATTCGGTCATTTTAACCTATGGGGGTAATTCG
35703968 GTCATTTTACCCTGTGGGGGTAATTCGGTCATTT
1 GTCATTTTACCCTGTGGGGGTAATTCGGTCATTT
35704002 ATTGACCTCT
Statistics
Matches: 274, Mismatches: 25, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
53 46 0.17
54 225 0.82
55 3 0.01
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (54 bp):
GTCATTTTACCCTGTGGGGGTAATTCGGTCATTTTAACCTATGGGGGTAATTCG
Found at i:35705470 original size:19 final size:20
Alignment explanation
Indices: 35705446--35705483 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
35705436 TGAGCTGATT
35705446 GGAGCTGAAA-TGAGCTAAG
1 GGAGCTGAAATTGAGCTAAG
35705465 GGAGCTGAAATTGAGCTAA
1 GGAGCTGAAATTGAGCTAA
35705484 AGTCAGCTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.37, C:0.11, G:0.34, T:0.18
Consensus pattern (20 bp):
GGAGCTGAAATTGAGCTAAG
Found at i:35706610 original size:27 final size:27
Alignment explanation
Indices: 35706563--35706614 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
35706553 TTTTCTCTTC
*
35706563 TTTCTTTTTCAATCTTTTCTTTTTCAG
1 TTTCTTTTTCAATCTTCTCTTTTTCAG
*
35706590 TTTCTTTTTCGATGC-TCTCTTTTTC
1 TTTCTTTTTCAAT-CTTCTCTTTTTC
35706615 TTTCACTTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.08, C:0.21, G:0.06, T:0.65
Consensus pattern (27 bp):
TTTCTTTTTCAATCTTCTCTTTTTCAG
Found at i:35711986 original size:5 final size:5
Alignment explanation
Indices: 35711965--35712037 Score: 80
Period size: 5 Copynumber: 14.4 Consensus size: 5
35711955 TTACTTTATT
35711965 TAATA TATATAA TAATA TAATA TAATA TAATA TAATA -AATA TAATA TAGTATA
1 TAATA TA-AT-A TAATA TAATA TAATA TAATA TAATA TAATA TAATA TA--ATA
*
35712018 TTATA TAATA -AA-A TAATA TA
1 TAATA TAATA TAATA TAATA TA
35712038 CATAACATAA
Statistics
Matches: 59, Mismatches: 2, Indels: 14
0.79 0.03 0.19
Matches are distributed among these distances:
3 1 0.02
4 8 0.14
5 39 0.66
6 4 0.07
7 7 0.12
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:35712034 original size:34 final size:36
Alignment explanation
Indices: 35711966--35712035 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
35711956 TACTTTATTT
35711966 AATATATATAATAATATAATATAATATAATATAATA
1 AATATATATAATAATATAATATAATATAATATAATA
* *
35712002 AATATAATATAGT-ATATTATATAATA-AA-ATAATA
1 AATAT-ATATAATAATATAATATAATATAATATAATA
35712036 TACATAACAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
34 6 0.19
35 2 0.06
36 17 0.55
37 6 0.19
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (36 bp):
AATATATATAATAATATAATATAATATAATATAATA
Found at i:35712047 original size:14 final size:13
Alignment explanation
Indices: 35711965--35712047 Score: 71
Period size: 14 Copynumber: 6.2 Consensus size: 13
35711955 TTACTTTATT
*
35711965 TAATAT-ATATAA
1 TAATATAATAAAA
35711977 TAATATAATATAATA
1 TAATATAATA-AA-A
35711992 TAATATAATAAATA
1 TAATATAATAAA-A
* *
35712006 TAATATAGT-ATA
1 TAATATAATAAAA
*
35712018 TTATATAATAAAA
1 TAATATAATAAAA
*
35712031 TAATATACATAACA
1 TAATATA-ATAAAA
35712045 TAA
1 TAA
35712048 AAATCTCATA
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
12 14 0.24
13 12 0.21
14 21 0.36
15 11 0.19
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.37
Consensus pattern (13 bp):
TAATATAATAAAA
Found at i:35717777 original size:22 final size:21
Alignment explanation
Indices: 35717752--35717795 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 21
35717742 TCTCTTTCTC
35717752 TGTTTCTATTTT-TTTCTTCTTT
1 TGTTTCT-TTTTCTTT-TTCTTT
35717774 TGTTTCTTTTTCTTTTTCTTT
1 TGTTTCTTTTTCTTTTTCTTT
35717795 T
1 T
35717796 ACTTCCTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.02, C:0.14, G:0.05, T:0.80
Consensus pattern (21 bp):
TGTTTCTTTTTCTTTTTCTTT
Found at i:35717996 original size:5 final size:5
Alignment explanation
Indices: 35717975--35718043 Score: 79
Period size: 5 Copynumber: 13.6 Consensus size: 5
35717965 TTACTTTATT
35717975 TAATA TATATAA TAATA TAATA TAATA TAATA TAATA TAATA T-ATAA
1 TAATA TA-AT-A TAATA TAATA TAATA TAATA TAATA TAATA TAAT-A
* *
35718022 TAAAA TAATA T-ATA TAACA TAA
1 TAATA TAATA TAATA TAATA TAA
35718044 AAATCTCATA
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
4 6 0.11
5 42 0.75
6 5 0.09
7 3 0.05
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (5 bp):
TAATA
Found at i:35724001 original size:50 final size:50
Alignment explanation
Indices: 35723937--35724070 Score: 153
Period size: 50 Copynumber: 2.7 Consensus size: 50
35723927 TCGATACACG
* * * *
35723937 TAGTAGCCTTCACATAGTACTAGACACGTGATCAAACTTTCCGGTATG-CA
1 TAGTAGCCTACACATAGTACTACACACGTGACCAAACATTCCGGTA-GACA
* * * *** *
35723987 TAGTAGCCTGCACATAGTACTACACATGCGACCTTTCATTCCGGTAGACG
1 TAGTAGCCTACACATAGTACTACACACGTGACCAAACATTCCGGTAGACA
35724037 TAGTAGCCTACACATAGTACTACACACGTGACCA
1 TAGTAGCCTACACATAGTACTACACACGTGACCA
35724071 TCACTTTCAA
Statistics
Matches: 69, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
49 1 0.01
50 68 0.99
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (50 bp):
TAGTAGCCTACACATAGTACTACACACGTGACCAAACATTCCGGTAGACA
Found at i:35726955 original size:25 final size:25
Alignment explanation
Indices: 35726875--35727164 Score: 212
Period size: 25 Copynumber: 11.6 Consensus size: 25
35726865 TAGCATCTTT
**
35726875 CCACAAAGGCTTTCAGAGAGAGTT-A
1 CCACAAAGGCTTT-TTAGAGAGTTCA
*
35726900 GCCACAAAGGCTTTCTATAG-GA-TTCG
1 -CCACAAAGGCTTT-T-TAGAGAGTTCA
* *
35726926 TCACAACGGCTTTTTAGAGAGTTCA
1 CCACAAAGGCTTTTTAGAGAGTTCA
* * *
35726951 CCACAAATG-TTTTTCAAAGATTTCA
1 CCACAAAGGCTTTTT-AGAGAGTTCA
*
35726976 -CAGCAAAGGCTTTTTAAAGAGTTCA
1 CCA-CAAAGGCTTTTTAGAGAGTTCA
* * * **
35727001 CCACCAAGGCTTTTCAGAGGGTTTG
1 CCACAAAGGCTTTTTAGAGAGTTCA
* *
35727026 CCTCAAAGGCTTTTTAGACAGTTCA
1 CCACAAAGGCTTTTTAGAGAGTTCA
* * *
35727051 CCATAAAGGCTTTTCAGAGAGTTCG
1 CCACAAAGGCTTTTTAGAGAGTTCA
* * * **
35727076 CCACAAAGGCATTTCATAGAGTTTG
1 CCACAAAGGCTTTTTAGAGAGTTCA
* * * **
35727101 CCACAAAGGCTTTTCAAAGATTTTG
1 CCACAAAGGCTTTTTAGAGAGTTCA
* *
35727126 CCACAAAGGATTTTTAGAGAGTTTA
1 CCACAAAGGCTTTTTAGAGAGTTCA
35727151 CCACAAAGGCTTTT
1 CCACAAAGGCTTTT
35727165 CAAATAATTT
Statistics
Matches: 212, Mismatches: 44, Indels: 17
0.78 0.16 0.06
Matches are distributed among these distances:
23 3 0.01
24 10 0.05
25 174 0.82
26 23 0.11
27 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (25 bp):
CCACAAAGGCTTTTTAGAGAGTTCA
Found at i:35727012 original size:75 final size:74
Alignment explanation
Indices: 35726902--35727166 Score: 241
Period size: 75 Copynumber: 3.5 Consensus size: 74
35726892 GAGAGTTAGC
** * * ** *
35726902 CACAAAGGCTTTCTATAG-GA-TTCGTCACAACGGCTTTTTAGAGAGTTCACCACAAATGTTTTT
1 CACAAAGGCTTT-T-TAGAGAGTTCACCACAAAGGCTTTTCAGAGAGTTTGCCACAAAGGTTTTT
35726965 CAAAGATTTCA
64 CAAAGATTTCA
* * * *
35726976 CAGCAAAGGCTTTTTAAAGAGTTCACCACCAAGGCTTTTCAGAGGGTTTGCCTCAAAGGCTTTTT
1 CA-CAAAGGCTTTTTAGAGAGTTCACCACAAAGGCTTTTCAGAGAGTTTGCCACAAAGG-TTTTT
* * *
35727041 -AGACAGTTCA
64 CAAAGATTTCA
* * * * * *
35727051 CCATAAAGGCTTTTCAGAGAGTTCGCCACAAAGGCATTTCATAGAGTTTGCCACAAAGGCTTTTC
1 -CACAAAGGCTTTTTAGAGAGTTCACCACAAAGGCTTTTCAGAGAGTTTGCCACAAAGGTTTTTC
35727116 AAAGATTTTGC-
65 AAAGA-TTT-CA
* *
35727127 CACAAAGGATTTTTAGAGAGTTTACCACAAAGGCTTTTCA
1 CACAAAGGCTTTTTAGAGAGTTCACCACAAAGGCTTTTCA
35727167 AATAATTTCG
Statistics
Matches: 150, Mismatches: 33, Indels: 15
0.76 0.17 0.08
Matches are distributed among these distances:
73 2 0.01
74 9 0.06
75 129 0.86
76 9 0.06
77 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (74 bp):
CACAAAGGCTTTTTAGAGAGTTCACCACAAAGGCTTTTCAGAGAGTTTGCCACAAAGGTTTTTCA
AAGATTTCA
Found at i:35727168 original size:50 final size:50
Alignment explanation
Indices: 35726875--35727168 Score: 274
Period size: 50 Copynumber: 5.9 Consensus size: 50
35726865 TAGCATCTTT
** * *
35726875 CCACAAAGGCTTTCAGAGAGAGTT-AGCCACAAAGGC-TTTCTATAG-GATTCG
1 CCACAAAGGCTTT-TTAGAGAGTTCA-CCACAAAGGCTTTTC-AAAGAG-TTTG
* * * *
35726926 TCACAACGGCTTTTTAGAGAGTTCACCACAAATGTTTTTCAAAGA-TTT-
1 CCACAAAGGCTTTTTAGAGAGTTCACCACAAAGGCTTTTCAAAGAGTTTG
* * * *
35726974 CACAGCAAAGGCTTTTTAAAGAGTTCACCACCAAGGCTTTTCAGAGGGTTTG
1 C-CA-CAAAGGCTTTTTAGAGAGTTCACCACAAAGGCTTTTCAAAGAGTTTG
* * * * *
35727026 CCTCAAAGGCTTTTTAGACAGTTCACCATAAAGGCTTTTCAGAGAGTTCG
1 CCACAAAGGCTTTTTAGAGAGTTCACCACAAAGGCTTTTCAAAGAGTTTG
* * * ** *
35727076 CCACAAAGGCATTTCATAGAGTTTGCCACAAAGGCTTTTCAAAGATTTTG
1 CCACAAAGGCTTTTTAGAGAGTTCACCACAAAGGCTTTTCAAAGAGTTTG
* *
35727126 CCACAAAGGATTTTTAGAGAGTTTACCACAAAGGCTTTTCAAA
1 CCACAAAGGCTTTTTAGAGAGTTCACCACAAAGGCTTTTCAAA
35727169 TAATTTCGTG
Statistics
Matches: 197, Mismatches: 39, Indels: 15
0.78 0.16 0.06
Matches are distributed among these distances:
49 4 0.02
50 172 0.87
51 20 0.10
52 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.29
Consensus pattern (50 bp):
CCACAAAGGCTTTTTAGAGAGTTCACCACAAAGGCTTTTCAAAGAGTTTG
Found at i:35728227 original size:26 final size:27
Alignment explanation
Indices: 35728198--35728260 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
35728188 TAATAACACA
**
35728198 GCAAAGCTGCCAGT-ACAGT-ATATGTG
1 GCAAAGCCACCAGTAACAGTAAT-TGTG
35728224 GCAAAGCCACCAGTAACAGTAATTGTG
1 GCAAAGCCACCAGTAACAGTAATTGTG
*
35728251 GCAGAGCCAC
1 GCAAAGCCAC
35728261 TAGAAACAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 12 0.38
27 18 0.56
28 2 0.06
ACGTcount: A:0.33, C:0.24, G:0.25, T:0.17
Consensus pattern (27 bp):
GCAAAGCCACCAGTAACAGTAATTGTG
Found at i:35728268 original size:27 final size:27
Alignment explanation
Indices: 35728212--35728268 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
35728202 AGCTGCCAGT
*
35728212 ACAGTATATGTGGCAAAGCCACCAGTA
1 ACAGTATATGTGGCAAAGCCACCAGAA
* *
35728239 ACAGTA-ATTGTGGCAGAGCCACTAGAA
1 ACAGTATA-TGTGGCAAAGCCACCAGAA
35728266 ACA
1 ACA
35728269 ATACTTCCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 1 0.04
27 25 0.96
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.18
Consensus pattern (27 bp):
ACAGTATATGTGGCAAAGCCACCAGAA
Found at i:35728462 original size:27 final size:27
Alignment explanation
Indices: 35728430--35728532 Score: 152
Period size: 27 Copynumber: 3.8 Consensus size: 27
35728420 ACCCATTAGG
*
35728430 ACCCATTGAGGGTATTTCAATAATTTT
1 ACCCATTGAGGGTATTTCAGTAATTTT
* *
35728457 ATCCATTGAGGGTATTTCGGTAATTTT
1 ACCCATTGAGGGTATTTCAGTAATTTT
*
35728484 ACCCATTAAGGGTATTTCAGTAATTTT
1 ACCCATTGAGGGTATTTCAGTAATTTT
* *
35728511 ACCCATCGAGGGTACTTCAGTA
1 ACCCATTGAGGGTATTTCAGTA
35728533 TAGTTAATGA
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 67 1.00
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (27 bp):
ACCCATTGAGGGTATTTCAGTAATTTT
Found at i:35740516 original size:25 final size:25
Alignment explanation
Indices: 35740474--35740526 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
35740464 TTTTCTCAAA
*
35740474 AATTTAATTAATATAAAATATTA-AT
1 AATTTAATAAATATAAAA-ATTAGAT
35740499 AATTTAATAAAT-TGAAAAATTAGAT
1 AATTTAATAAATAT-AAAAATTAGAT
35740524 AAT
1 AAT
35740527 AAAATTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.40
Consensus pattern (25 bp):
AATTTAATAAATATAAAAATTAGAT
Found at i:35741854 original size:32 final size:32
Alignment explanation
Indices: 35741814--35742020 Score: 193
Period size: 32 Copynumber: 6.5 Consensus size: 32
35741804 TGTGATTAGT
*
35741814 ACAAAGCCATCAGTAACAGTGATATGATCGAC
1 ACAAAGCCATCAGTAACAGTGATATGATCGGC
* * * *
35741846 ACACAGCCATCAGTAACGGTAACATGATCGGC
1 ACAAAGCCATCAGTAACAGTGATATGATCGGC
* *
35741878 ACAAAGCCCTCAGTAGCAGTGATATGATCGGC
1 ACAAAGCCATCAGTAACAGTGATATGATCGGC
* * * * * *
35741910 ACACAGCCATTAATAACAGTGAAATGATCAGT
1 ACAAAGCCATCAGTAACAGTGATATGATCGGC
* * ** * *
35741942 A-ACCAGCCGTTGGTAACGGTAATATGATCGGC
1 ACA-AAGCCATCAGTAACAGTGATATGATCGGC
* *
35741974 ACAAAGCCATCAGTAACGGT-ACTATGATCGTC
1 ACAAAGCCATCAGTAACAGTGA-TATGATCGGC
35742006 ACAAAGCCATCAGTA
1 ACAAAGCCATCAGTA
35742021 GCATTGCAGC
Statistics
Matches: 140, Mismatches: 32, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
31 2 0.01
32 137 0.98
33 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (32 bp):
ACAAAGCCATCAGTAACAGTGATATGATCGGC
Found at i:35741898 original size:64 final size:64
Alignment explanation
Indices: 35741814--35742020 Score: 222
Period size: 64 Copynumber: 3.2 Consensus size: 64
35741804 TGTGATTAGT
*
35741814 ACAAAGCCATCAGTAACAGTGATATGATCGACACACAGCCATCAGTAACGGTAACATGATCGGC
1 ACAAAGCCATCAGTAACAGTGATATGATCGGCACACAGCCATCAGTAACGGTAACATGATCGGC
* * * * * * *
35741878 ACAAAGCCCTCAGTAGCAGTGATATGATCGGCACACAGCCATTAATAACAGTGAA-ATGATCAGT
1 ACAAAGCCATCAGTAACAGTGATATGATCGGCACACAGCCATCAGTAACGGT-AACATGATCGGC
* * ** * * * *
35741942 A-ACCAGCCGTTGGTAACGGTAATATGATCGGCACAAAGCCATCAGTAACGGT-ACTATGATCGT
1 ACA-AAGCCATCAGTAACAGTGATATGATCGGCACACAGCCATCAGTAACGGTAAC-ATGATCGG
35742005 C
64 C
35742006 ACAAAGCCATCAGTA
1 ACAAAGCCATCAGTA
35742021 GCATTGCAGC
Statistics
Matches: 112, Mismatches: 26, Indels: 10
0.76 0.18 0.07
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 107 0.96
65 3 0.03
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (64 bp):
ACAAAGCCATCAGTAACAGTGATATGATCGGCACACAGCCATCAGTAACGGTAACATGATCGGC
Found at i:35742075 original size:26 final size:26
Alignment explanation
Indices: 35742026--35742076 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
35742016 CAGTAGCATT
* *
35742026 GCAGCAAAGTTGCCAGCGACAGTATC
1 GCAGCAAAGCTGCCAGCAACAGTATC
* *
35742052 GCAGCAAAGCTGCCAGTAATAGTAT
1 GCAGCAAAGCTGCCAGCAACAGTAT
35742077 ATGTGGCCGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.33, C:0.24, G:0.25, T:0.18
Consensus pattern (26 bp):
GCAGCAAAGCTGCCAGCAACAGTATC
Found at i:35742373 original size:26 final size:27
Alignment explanation
Indices: 35742317--35742472 Score: 190
Period size: 27 Copynumber: 5.9 Consensus size: 27
35742307 TATGAGGGTA
* * *
35742317 TACCCTACGGGGGTATTACGGTTATTT
1 TACCCTATGGGGGTATTTCGGTCATTT
* *
35742344 TACCCTATGGGGGTATTTC-ATCATTC
1 TACCCTATGGGGGTATTTCGGTCATTT
*
35742370 TACCCTATGGGGGTATTTCGGCCATTT
1 TACCCTATGGGGGTATTTCGGTCATTT
* *
35742397 TGCCCTAT-GGGGTATTTCTGTCATTT
1 TACCCTATGGGGGTATTTCGGTCATTT
* **
35742423 TACCTTATAAGGGTATTTCGGTCATTT
1 TACCCTATGGGGGTATTTCGGTCATTT
*
35742450 TACCCTTTGGGGGTATTTCGGTC
1 TACCCTATGGGGGTATTTCGGTC
35742473 CAGATATCGC
Statistics
Matches: 108, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
26 45 0.42
27 63 0.58
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.40
Consensus pattern (27 bp):
TACCCTATGGGGGTATTTCGGTCATTT
Found at i:35742397 original size:53 final size:54
Alignment explanation
Indices: 35742317--35742468 Score: 191
Period size: 53 Copynumber: 2.9 Consensus size: 54
35742307 TATGAGGGTA
* * *
35742317 TACCCTACGGGGGTATTACGGTTATTTTACCCTATGGGGGTATTTC-ATCATTC
1 TACCCTATGGGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTCTATCATTC
* * * *
35742370 TACCCTATGGGGGTATTTCGGCCATTTTGCCCTAT-GGGGTATTTCTGTCATTT
1 TACCCTATGGGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTCTATCATTC
* ** *
35742423 TACCTTATAAGGGTATTTCGGTCATTTTACCCTTTGGGGGTATTTC
1 TACCCTATGGGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTC
35742469 GGTCCAGATA
Statistics
Matches: 84, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
52 10 0.12
53 64 0.76
54 10 0.12
ACGTcount: A:0.16, C:0.20, G:0.23, T:0.41
Consensus pattern (54 bp):
TACCCTATGGGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTCTATCATTC
Found at i:35743454 original size:30 final size:30
Alignment explanation
Indices: 35743397--35743456 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
35743387 GCTTTTTTAA
* *
35743397 AATATTTACAAAAAGAGGCATCTAATTTTT
1 AATATTTACAAAAAGAGGCACCAAATTTTT
35743427 AATATTTACAAAAAGA-GCAACCAAATTTTT
1 AATATTTACAAAAAGAGGC-ACCAAATTTTT
35743457 TAAAATAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 2 0.07
30 25 0.93
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.33
Consensus pattern (30 bp):
AATATTTACAAAAAGAGGCACCAAATTTTT
Found at i:35750988 original size:12 final size:12
Alignment explanation
Indices: 35750971--35750996 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
35750961 AATATTCATC
35750971 AAAATTAATTAA
1 AAAATTAATTAA
35750983 AAAATTAATTAA
1 AAAATTAATTAA
35750995 AA
1 AA
35750997 TTCAACATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAATTAATTAA
Found at i:35772680 original size:22 final size:22
Alignment explanation
Indices: 35772652--35772804 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
35772642 TTTATTGTTC
*
35772652 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
35772674 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
35772696 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
35772718 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
35772740 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
*
35772762 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
35772784 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
35772805 ACTATCAACA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:35773083 original size:33 final size:33
Alignment explanation
Indices: 35773046--35773188 Score: 109
Period size: 33 Copynumber: 4.2 Consensus size: 33
35773036 ATATGGTGGG
*
35773046 ATCAGCACTTAGCAACCACCAATGAATCTGGGA
1 ATCAGCACTTAGCAACCACCAATGAATCGGGGA
** *
35773079 ATCAGCACACAGCAACC-CC--T---TGGGGGA
1 ATCAGCACTTAGCAACCACCAATGAATCGGGGA
* *
35773106 ATCAGCACTTAGCAACCCCCTTCACATTTCAGATGCGGTGGA
1 ATCAGCACTTAGCAA-CCAC--CA-A--TGA-AT-CGG-GGA
35773148 ATCAGCACTTAGCAACCACCAATGAATCGGGGA
1 ATCAGCACTTAGCAACCACCAATGAATCGGGGA
35773181 ATCAGCAC
1 ATCAGCAC
35773189 ACAACAACCC
Statistics
Matches: 86, Mismatches: 9, Indels: 30
0.69 0.07 0.24
Matches are distributed among these distances:
27 18 0.21
28 2 0.02
29 1 0.01
30 1 0.01
31 1 0.01
32 2 0.02
33 26 0.30
34 3 0.03
35 2 0.02
36 3 0.03
38 1 0.01
39 2 0.02
40 1 0.01
41 5 0.06
42 18 0.21
ACGTcount: A:0.32, C:0.30, G:0.20, T:0.17
Consensus pattern (33 bp):
ATCAGCACTTAGCAACCACCAATGAATCGGGGA
Found at i:35773181 original size:102 final size:103
Alignment explanation
Indices: 35772955--35773201 Score: 370
Period size: 102 Copynumber: 2.4 Consensus size: 103
35772945 GAAGAAGCAC
* * ** * *
35772955 CAACCACCAATGAATAGGGGAATTAGCACTTAGCAACCCCTCGGTGGAATCAGCACTTAGCAACC
1 CAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGGGAATCAGCACTTAGCAACC
* *
35773020 CCCTTTCACATTTAAAATATGGTGGGATCAGCACTTAG
66 CCCTTTCACATTTAAAATACGGTGGAATCAGCACTTAG
*
35773058 CAACCACCAATGAATCTGGGAATCAGCACACAGCAACCCCTTGGGGGAATCAGCACTTAGCAACC
1 CAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGGGAATCAGCACTTAGCAACC
* * *
35773123 CCC-TTCACATTTCAGATGCGGTGGAATCAGCACTTAG
66 CCCTTTCACATTTAAAATACGGTGGAATCAGCACTTAG
*
35773160 CAACCACCAATGAATCGGGGAATCAGCACACAACAACCCCTT
1 CAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTT
35773202 TATATGCAAT
Statistics
Matches: 130, Mismatches: 14, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
102 69 0.53
103 61 0.47
ACGTcount: A:0.32, C:0.30, G:0.19, T:0.19
Consensus pattern (103 bp):
CAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGGGAATCAGCACTTAGCAACC
CCCTTTCACATTTAAAATACGGTGGAATCAGCACTTAG
Found at i:35774537 original size:41 final size:41
Alignment explanation
Indices: 35774481--35774583 Score: 134
Period size: 41 Copynumber: 2.5 Consensus size: 41
35774471 TGATTTGATA
* * * *
35774481 CACCGGCTTTTAGCCTGCTAGACCTATAGTCCGAAATGTAT
1 CACCGGCATTAAGCCTGCTAGACCTAAAGTCCGAAATATAT
* * * *
35774522 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAATTATTT
1 CACCGGCATTAAGCCTGCTAGACCTAAAGTCCGAAATATAT
35774563 CACCGGCATTAAGCCTGCTAG
1 CACCGGCATTAAGCCTGCTAG
35774584 GCACATAGCC
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.27
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACCTAAAGTCCGAAATATAT
Found at i:35774597 original size:41 final size:41
Alignment explanation
Indices: 35774521--35774598 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
35774511 CCGAAATGTA
** *
35774521 TCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAATTATT
1 TCACCGGCATTAAGCCTGCTAGACACAAAGCCTGAATTATT
* *
35774562 TCACCGGCATTAAGCCTGCTAGGCACATAGCCTGAAT
1 TCACCGGCATTAAGCCTGCTAGACACAAAGCCTGAAT
35774599 AACTCAAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (41 bp):
TCACCGGCATTAAGCCTGCTAGACACAAAGCCTGAATTATT
Found at i:35775177 original size:2 final size:2
Alignment explanation
Indices: 35775170--35775203 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
35775160 ATAGATTTTC
35775170 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35775204 TCTTAGTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35775666 original size:13 final size:13
Alignment explanation
Indices: 35775648--35775672 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35775638 TCAAACTATC
35775648 AAATTTTCACACG
1 AAATTTTCACACG
35775661 AAATTTTCACAC
1 AAATTTTCACAC
35775673 ATATAACTTA
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:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:35781873 original size:41 final size:41
Alignment explanation
Indices: 35781817--35781919 Score: 134
Period size: 41 Copynumber: 2.5 Consensus size: 41
35781807 TGATTCGATA
* * * *
35781817 CACCGGCTTTTAGCCTGCTAGACCTATAGTCCGAAATGTAT
1 CACCGGCATTAAGCCTGCTAGACCTAAAGTCCGAAATATAT
* * * *
35781858 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAATTATTT
1 CACCGGCATTAAGCCTGCTAGACCTAAAGTCCGAAATATAT
35781899 CACCGGCATTAAGCCTGCTAG
1 CACCGGCATTAAGCCTGCTAG
35781920 GCACATAGCC
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.27
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACCTAAAGTCCGAAATATAT
Found at i:35781933 original size:41 final size:41
Alignment explanation
Indices: 35781857--35781934 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
35781847 CCGAAATGTA
** *
35781857 TCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAATTATT
1 TCACCGGCATTAAGCCTGCTAGACACAAAGCCTGAATTATT
* *
35781898 TCACCGGCATTAAGCCTGCTAGGCACATAGCCTGAAT
1 TCACCGGCATTAAGCCTGCTAGACACAAAGCCTGAAT
35781935 AACTCAAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (41 bp):
TCACCGGCATTAAGCCTGCTAGACACAAAGCCTGAATTATT
Found at i:35782214 original size:66 final size:65
Alignment explanation
Indices: 35782074--35782294 Score: 166
Period size: 65 Copynumber: 3.3 Consensus size: 65
35782064 TACATGATTC
* * * * * *
35782074 ATAACATTAAATTCAACTCAAGAAAC-TCAAATCCTATCA-TCAATCCACATGTATAATTATATA
1 ATAACATTAAGTTCAACTCAAGAAACATTACATCAT-TTATTCAAACCACA--TAT-A-TATATA
*
35782137 TAATT
61 TATTT
* ** * *
35782142 ATTAACATTAAGTTCAGCTCGAAGAAAC-TTGTATC-TTATATTCAAACCTCTTATATATATATA
1 A-TAACATTAAGTTCAACTC-AAGAAACATTACATCATT-TATTCAAACCACATATATATATATA
35782205 TTT
63 TTT
* * *
35782208 CATAACATTACA-TTCAATTCAA-AAACATTACATCATTTATTCGAACCACATATATATATACAA
1 -ATAACATTA-AGTTCAACTCAAGAAACATTACATCATTTATTCAAACCACATATATATATA-TA
35782271 TTT
63 TTT
35782274 ATAACATTAAGTTCAACTCAA
1 ATAACATTAAGTTCAACTCAA
35782295 AGAATTTGTA
Statistics
Matches: 124, Mismatches: 19, Indels: 23
0.75 0.11 0.14
Matches are distributed among these distances:
64 5 0.04
65 45 0.36
66 30 0.24
67 3 0.02
68 5 0.04
69 18 0.15
70 18 0.15
ACGTcount: A:0.43, C:0.18, G:0.04, T:0.35
Consensus pattern (65 bp):
ATAACATTAAGTTCAACTCAAGAAACATTACATCATTTATTCAAACCACATATATATATATATTT
Found at i:35782495 original size:2 final size:2
Alignment explanation
Indices: 35782488--35782517 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
35782478 ATAGATTTCC
35782488 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35782518 TCTAGTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35783482 original size:13 final size:13
Alignment explanation
Indices: 35783464--35783488 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35783454 TCAAACTATC
35783464 AAATTTTCACACG
1 AAATTTTCACACG
35783477 AAATTTTCACAC
1 AAATTTTCACAC
35783489 ATATAACTTA
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:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:35789682 original size:15 final size:15
Alignment explanation
Indices: 35789662--35789690 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
35789652 TTTTAAAAGG
35789662 TTTTGATTTGATAAA
1 TTTTGATTTGATAAA
35789677 TTTTGATTTGATAA
1 TTTTGATTTGATAA
35789691 TCGAGACCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (15 bp):
TTTTGATTTGATAAA
Found at i:35791113 original size:35 final size:34
Alignment explanation
Indices: 35790973--35791151 Score: 107
Period size: 33 Copynumber: 5.3 Consensus size: 34
35790963 TATTCAAACA
* * *
35790973 TAAGACCATGGTTGGACCATGGAAGTGTTTATATG
1 TAAGACCATAGTTGGACCATGGCA-TGTTTAGATG
* * * * *
35791008 TAAGGCCATAGTTGGGCTATAGCAT-TCT-GATG
1 TAAGACCATAGTTGGACCATGGCATGTTTAGATG
* * *** * * *
35791040 ATAAGACAATAATTGGGTTATGGCA-CTATAGACG
1 -TAAGACCATAGTTGGACCATGGCATGTTTAGATG
*
35791074 TAAGACCATAGTTGGACCATGGCAGTGTTTATATG
1 TAAGACCATAGTTGGACCATGGCA-TGTTTAGATG
* * *
35791109 TAAGACCATAGCTGGGCTATGGCAT-TTT-GATG
1 TAAGACCATAGTTGGACCATGGCATGTTTAGATG
35791141 ATAAGACCATA
1 -TAAGACCATA
35791152 ACTGGGTTAT
Statistics
Matches: 110, Mismatches: 28, Indels: 14
0.72 0.18 0.09
Matches are distributed among these distances:
32 6 0.05
33 55 0.50
34 5 0.05
35 44 0.40
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.30
Consensus pattern (34 bp):
TAAGACCATAGTTGGACCATGGCATGTTTAGATG
Found at i:35791151 original size:33 final size:33
Alignment explanation
Indices: 35791005--35791167 Score: 123
Period size: 33 Copynumber: 4.9 Consensus size: 33
35790995 AAGTGTTTAT
* * *
35791005 ATGTAAGGCCATAGTTGGGCTATAGCA-TTCTG
1 ATGTAAGACCATAGTTGGGCTATGGCACTTTTG
* * * * *
35791037 ATGATAAGACAATAATTGGGTTATGGCACTATAG
1 ATG-TAAGACCATAGTTGGGCTATGGCACTTTTG
* * * * *
35791071 ACGTAAGACCATAGTTGGACCATGGCAGTGTTTAT
1 ATGTAAGACCATAGTTGGGCTATGGCACT-TTT-G
*
35791106 ATGTAAGACCATAGCTGGGCTATGGCA-TTTTG
1 ATGTAAGACCATAGTTGGGCTATGGCACTTTTG
** *
35791138 ATGATAAGACCATAACTGGGTTATGGCACT
1 ATG-TAAGACCATAGTTGGGCTATGGCACT
35791168 ACGAATGTAC
Statistics
Matches: 100, Mismatches: 25, Indels: 10
0.74 0.19 0.07
Matches are distributed among these distances:
32 6 0.06
33 64 0.64
34 7 0.07
35 23 0.23
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (33 bp):
ATGTAAGACCATAGTTGGGCTATGGCACTTTTG
Found at i:35791182 original size:101 final size:101
Alignment explanation
Indices: 35790973--35791228 Score: 329
Period size: 101 Copynumber: 2.6 Consensus size: 101
35790963 TATTCAAACA
* * *
35790973 TAAGACCATGGTTGGACCATGGAAGTGTTTATATGTAAGGCCATAGTTGGGCTATAGCATTCTGA
1 TAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGTTGGGCTATGGCATTCTGA
* *
35791038 TGATAAGACAATAATTGGGTTATGGCACTATAGACG
66 TGATAAGACAATAACTGGGTTATGGCACTAGAGACG
* * *
35791074 TAAGACCATAGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGCTGGGCTATGGCATTTTGA
1 TAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGTTGGGCTATGGCATTCTGA
* *
35791139 TGATAAGACCATAACTGGGTTATGGCACTACGA-ATG
66 TGATAAGACAATAACTGGGTTATGGCACTA-GAGACG
* ** * * * *
35791175 TACGACCATGGCAGGGCCATGGCAATG--CATATGTAAGACCATAGTTGGACTATG
1 TAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGTTGGGCTATG
35791229 ACAAAAATGA
Statistics
Matches: 135, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
99 24 0.18
101 110 0.81
102 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.28
Consensus pattern (101 bp):
TAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGTTGGGCTATGGCATTCTGA
TGATAAGACAATAACTGGGTTATGGCACTAGAGACG
Found at i:35794361 original size:35 final size:35
Alignment explanation
Indices: 35794307--35794429 Score: 158
Period size: 35 Copynumber: 3.5 Consensus size: 35
35794297 TACACAGTTA
* *
35794307 ACCATTCAGCACACAAGATGTTCATAAGAGCTAGT
1 ACCATCCAGCACACCAGATGTTCATAAGAGCTAGT
* * *
35794342 ACCACCCAGCACACCAGATGCTT-ACAAGAGTTAGT
1 ACCATCCAGCACACCAGATG-TTCATAAGAGCTAGT
* * *
35794377 ACCATCCAACACACCAGATGCTCATAAGAGCCAGT
1 ACCATCCAGCACACCAGATGTTCATAAGAGCTAGT
35794412 ACCATCCAGCACACCAGA
1 ACCATCCAGCACACCAGA
35794430 AACACTGTAA
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
34 1 0.01
35 71 0.96
36 2 0.03
ACGTcount: A:0.37, C:0.32, G:0.15, T:0.16
Consensus pattern (35 bp):
ACCATCCAGCACACCAGATGTTCATAAGAGCTAGT
Found at i:35799395 original size:27 final size:27
Alignment explanation
Indices: 35799302--35799418 Score: 92
Period size: 27 Copynumber: 4.3 Consensus size: 27
35799292 TCATGGGCAG
*
35799302 ATGACCGAAATACCTCCATAAAGGGTAAA
1 ATGACCGAAATACC-CC-CAAAGGGTAAA
* *
35799331 ATAACCGAAATACCCCCGAAGGGTAAA
1 ATGACCGAAATACCCCCAAAGGGTAAA
*** ****
35799358 ATGATTAAAATTTTGCCAAAGGGTAAA
1 ATGACCGAAATACCCCCAAAGGGTAAA
**
35799385 ATGACCGAAATACCCTTGAAA-GGTAAA
1 ATGACCGAAATACCC-CCAAAGGGTAAA
35799412 ATGACCG
1 ATGACCG
35799419 GCACTATTAT
Statistics
Matches: 66, Mismatches: 21, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
27 48 0.73
28 5 0.08
29 13 0.20
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.19
Consensus pattern (27 bp):
ATGACCGAAATACCCCCAAAGGGTAAA
Found at i:35799501 original size:28 final size:28
Alignment explanation
Indices: 35799461--35799522 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
35799451 GTTACATTAT
*
35799461 CACACTGTTACTGTATTAG-GCTAAGGCC
1 CACACTATTACTGTA-TAGAGCTAAGGCC
*
35799489 CACACTATTACTGTATCGAGCTAAGGCC
1 CACACTATTACTGTATAGAGCTAAGGCC
35799517 CACACT
1 CACACT
35799523 GTACTATTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 2 0.06
28 29 0.94
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.26
Consensus pattern (28 bp):
CACACTATTACTGTATAGAGCTAAGGCC
Found at i:35799557 original size:33 final size:33
Alignment explanation
Indices: 35799492--35799557 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
35799482 TAAGGCCCAC
* * *
35799492 ACTATTACTGTATCGAGCTAAGGCCCACACTGT
1 ACTATTACTGCATAGAGCTAAGGCCCAAACTGT
* * *
35799525 ACTATTACTGCATAGGGCTCAGGCCTAAACTGT
1 ACTATTACTGCATAGAGCTAAGGCCCAAACTGT
35799558 TACTGCATGT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (33 bp):
ACTATTACTGCATAGAGCTAAGGCCCAAACTGT
Found at i:35805376 original size:27 final size:27
Alignment explanation
Indices: 35805345--35805443 Score: 126
Period size: 27 Copynumber: 3.6 Consensus size: 27
35805335 GGGTAGATGT
*
35805345 CCGAAATACCCCTGAAGGGTAAAATGG
1 CCGAAATACCCCTGAAGGGTAAAATGA
*
35805372 CCGAAATACCCCCGAAGGGTAAAATGA
1 CCGAAATACCCCTGAAGGGTAAAATGA
* * *
35805399 CCAAAATACCCCTAAAAGGTAAAATGA
1 CCGAAATACCCCTGAAGGGTAAAATGA
**
35805426 CCGTTATACCCCTAGAAG
1 CCGAAATACCCCT-GAAG
35805444 TCGAAATGAC
Statistics
Matches: 60, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
27 58 0.97
28 2 0.03
ACGTcount: A:0.40, C:0.25, G:0.19, T:0.15
Consensus pattern (27 bp):
CCGAAATACCCCTGAAGGGTAAAATGA
Found at i:35816591 original size:19 final size:19
Alignment explanation
Indices: 35816547--35816613 Score: 107
Period size: 19 Copynumber: 3.5 Consensus size: 19
35816537 AAGTGCAAAT
*
35816547 CAGGGGTACCGAAGTACAA
1 CAGGGGTACCAAAGTACAA
35816566 TCAGGGGTACCAAAGTACAA
1 -CAGGGGTACCAAAGTACAA
*
35816586 CAGGGGCACCAAAGTACAA
1 CAGGGGTACCAAAGTACAA
35816605 CAGGGGTAC
1 CAGGGGTAC
35816614 GTATGTGCGA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
19 26 0.59
20 18 0.41
ACGTcount: A:0.37, C:0.22, G:0.30, T:0.10
Consensus pattern (19 bp):
CAGGGGTACCAAAGTACAA
Found at i:35817411 original size:14 final size:14
Alignment explanation
Indices: 35817394--35817420 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
35817384 TTTTACTTAG
35817394 TTTATTTATTAAAA
1 TTTATTTATTAAAA
35817408 TTTATTTATTAAA
1 TTTATTTATTAAA
35817421 CTACAACTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTATTTATTAAAA
Found at i:35818329 original size:25 final size:23
Alignment explanation
Indices: 35818293--35818342 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
35818283 AGTTAATAAT
35818293 AATTCTCTTTGAGCTTTTCTTTAAG
1 AATTCTCTTTGAG--TTTCTTTAAG
*
35818318 AATTGCTC-TTGAGTTTCTTTTAG
1 AATT-CTCTTTGAGTTTCTTTAAG
35818341 AA
1 AA
35818343 GTTGTTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 11 0.48
25 9 0.39
26 3 0.13
ACGTcount: A:0.22, C:0.14, G:0.14, T:0.50
Consensus pattern (23 bp):
AATTCTCTTTGAGTTTCTTTAAG
Found at i:35829023 original size:16 final size:16
Alignment explanation
Indices: 35828999--35829050 Score: 70
Period size: 15 Copynumber: 3.1 Consensus size: 16
35828989 CTTTTGAAAC
35828999 TTTTAAATTTTTTATAA
1 TTTT-AATTTTTTATAA
35829016 TTTTAA-TTTTTATAA
1 TTTTAATTTTTTATAA
35829031 TTTTTAACTTTTTTATAA
1 -TTTTAA-TTTTTTATAA
35829049 TT
1 TT
35829051 AAGATTAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
15 9 0.28
16 8 0.25
17 6 0.19
18 9 0.28
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTAATTTTTTATAA
Found at i:35829036 original size:33 final size:32
Alignment explanation
Indices: 35828966--35829050 Score: 100
Period size: 33 Copynumber: 2.6 Consensus size: 32
35828956 GGTACAAAAT
* *
35828966 CTTTAAAATGTTTTTAT-ATTTTACTTTTGAAA
1 CTTTTAAAT-TTTTTATAATTTTAATTTTGAAA
*
35828998 CTTTTAAATTTTTTATAATTTTAATTTTTATAA
1 CTTTTAAATTTTTTATAATTTTAATTTTGA-AA
* *
35829031 TTTTTAACTTTTTTATAATT
1 CTTTTAAATTTTTTATAATT
35829051 AAGATTAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
31 7 0.15
32 19 0.41
33 20 0.43
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (32 bp):
CTTTTAAATTTTTTATAATTTTAATTTTGAAA
Found at i:35841669 original size:23 final size:23
Alignment explanation
Indices: 35841614--35841669 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
35841604 ACGCGGAATG
*
35841614 TTTTGTAAAGCCTTTATGGCATA
1 TTTTGTAAAGCCTGTATGGCATA
** * *
35841637 TTCGGCAAAGCCTGTATGGTATA
1 TTTTGTAAAGCCTGTATGGCATA
35841660 TTTTGTAAAG
1 TTTTGTAAAG
35841670 ATTTTGTGGC
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.39
Consensus pattern (23 bp):
TTTTGTAAAGCCTGTATGGCATA
Found at i:35841691 original size:23 final size:23
Alignment explanation
Indices: 35841665--35841730 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 23
35841655 GTATATTTTG
35841665 TAAAGATTTTGTGGCATATTCTA
1 TAAAGATTTTGTGGCATATTCTA
* ** *
35841688 TAAAG-TCTTTGGGGTGTGTTCTA
1 TAAAGAT-TTTGTGGCATATTCTA
35841711 TAAAGCA-TTTGTGGCATATT
1 TAAAG-ATTTTGTGGCATATT
35841731 TTGTGGCGTC
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
22 1 0.03
23 31 0.97
ACGTcount: A:0.26, C:0.09, G:0.23, T:0.42
Consensus pattern (23 bp):
TAAAGATTTTGTGGCATATTCTA
Found at i:35844447 original size:51 final size:49
Alignment explanation
Indices: 35844358--35844538 Score: 172
Period size: 51 Copynumber: 3.6 Consensus size: 49
35844348 GTTCACATAA
* * * *
35844358 TAGCCTGCACATAGTATTTA-ACATGTGACCATCACTATCCGATACACGTAG
1 TAGCCTGCACATAGTA-CTACACACGTGA-CAAC-CTATCCGGTACACGTAG
* * * * *
35844409 TAGCCTACACGTAGTACTACACACGTGATCGAAGCTATCCGGTACGCATAG
1 TAGCCTGCACATAGTACTACACACGTGA-C-AACCTATCCGGTACACGTAG
35844460 TAGCCTGCACATAGTACTACACA--TG-CAACCTATCATTCTGGTACACGTAG
1 TAGCCTGCACATAGTACTACACACGTGACAACCTATC---C-GGTACACGTAG
35844510 TAGCCTGCACATAGTACTACACACGTGAC
1 TAGCCTGCACATAGTACTACACACGTGAC
35844539 CATCACTTTC
Statistics
Matches: 106, Mismatches: 15, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
46 7 0.07
47 1 0.01
49 3 0.03
50 34 0.32
51 57 0.54
52 3 0.03
53 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (49 bp):
TAGCCTGCACATAGTACTACACACGTGACAACCTATCCGGTACACGTAG
Found at i:35844561 original size:101 final size:102
Alignment explanation
Indices: 35844345--35844537 Score: 248
Period size: 101 Copynumber: 1.9 Consensus size: 102
35844335 ATTAATGATA
* * **
35844345 CCGGTTCACATAATAGCCTGCACATAGTATTTAACATGTGACCATCACTATCCGATACACGTAGT
1 CCGGTTCACATAGTAGCCTGCACATAGTATCTAACATGCAACCATCACTATCCGATACACGTAGT
* *
35844410 AGCCTACACGTAGTACTACACACGTGATCGAAGCTAT
66 AGCCTACACATAGTACTACACACGTGATCCAAGCTAT
* * * *
35844447 CCGGTACGCATAGTAGCCTGCACATAGTA-CTACACATGCAACCTATCA-T-TCTGGTACACGTA
1 CCGGTTCACATAGTAGCCTGCACATAGTATCTA-ACATGCAACC-ATCACTATCCGATACACGTA
*
35844509 GTAGCCTGCACATAGTACTACACACGTGA
64 GTAGCCTACACATAGTACTACACACGTGA
35844538 CCATCACTTT
Statistics
Matches: 79, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
101 40 0.51
102 35 0.44
103 4 0.05
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (102 bp):
CCGGTTCACATAGTAGCCTGCACATAGTATCTAACATGCAACCATCACTATCCGATACACGTAGT
AGCCTACACATAGTACTACACACGTGATCCAAGCTAT
Found at i:35847753 original size:42 final size:42
Alignment explanation
Indices: 35847673--35847754 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
35847663 CGTTTTCTCT
* **
35847673 ATGCCATAGTCCAACTATGGTCTTACACATATTTACATATTG
1 ATGCCATAGCCCAACTATGGTCTTACACATATGCACATATTG
*
35847715 ATGCCATAGCCCAGCTATGGTCTTACACA-ATAGCACATAT
1 ATGCCATAGCCCAACTATGGTCTTACACATAT-GCACATAT
35847755 CACACCGATG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 2 0.06
42 33 0.94
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.30
Consensus pattern (42 bp):
ATGCCATAGCCCAACTATGGTCTTACACATATGCACATATTG
Found at i:35850489 original size:51 final size:50
Alignment explanation
Indices: 35850404--35850599 Score: 202
Period size: 51 Copynumber: 3.9 Consensus size: 50
35850394 TTAACGATAC
* * * *
35850404 CGGTTCACATAGTAGCCTACACATGGTACTACACATGTGACCATCACTATT
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAT-ACTATT
* * * * *
35850455 CGATACACGTAGTAGCCTGTACATAGTACTACACACGTGATCGA-AGCTATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGA-CCATA-CTATT
* * *
35850506 CGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACC-TA-TCATT
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCATACT-ATT
35850555 CTGGTACACGTAGTAGCCTGCACATAGTACTACACAAT-TGACCAT
1 C-GGTACACGTAGTAGCCTGCACATAGTACTACAC-ATGTGACCAT
35850600 CACTTTCACT
Statistics
Matches: 118, Mismatches: 20, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
48 1 0.01
49 3 0.03
50 38 0.32
51 74 0.63
52 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (50 bp):
CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCATACTATT
Found at i:35850623 original size:101 final size:102
Alignment explanation
Indices: 35850403--35850591 Score: 258
Period size: 102 Copynumber: 1.9 Consensus size: 102
35850393 ATTAACGATA
* *
35850403 CCGGTTCACATAGTAGCCTACACATGGTACTACACATGTGACCATCACTATTCGATACACGTAGT
1 CCGGTTCACATAGTAGCCTACACATAGTACTACACATGCGACCATCACTATTCGATACACGTAGT
* * *
35850468 AGCCTGTACATAGTACTACACACGTGATCGAAGCTAT
66 AGCCTGCACATAGTACTACACAAGTGATCCAAGCTAT
* * * *
35850505 CCGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACC-T-A-TCATTCTGGTACACGTA
1 CCGGTTCACATAGTAGCCTACACATAGTACTACACATGCGACCATCACT-ATTC-GATACACGTA
35850567 GTAGCCTGCACATAGTACTACACAA
64 GTAGCCTGCACATAGTACTACACAA
35850592 TTGACCATCA
Statistics
Matches: 77, Mismatches: 8, Indels: 5
0.86 0.09 0.06
Matches are distributed among these distances:
99 1 0.01
100 5 0.06
101 33 0.43
102 38 0.49
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (102 bp):
CCGGTTCACATAGTAGCCTACACATAGTACTACACATGCGACCATCACTATTCGATACACGTAGT
AGCCTGCACATAGTACTACACAAGTGATCCAAGCTAT
Found at i:35861084 original size:24 final size:25
Alignment explanation
Indices: 35861057--35861109 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
35861047 TATATATATA
35861057 TTTTATTTTG-TTTTTATTTTGTTT-
1 TTTTATTTTGTTTTTTATTTT-TTTC
35861081 TTTTATTTTGTTTTTTATTTTTTTC
1 TTTTATTTTGTTTTTTATTTTTTTC
35861106 TTTT
1 TTTT
35861110 GGTGCAGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
24 13 0.48
25 14 0.52
ACGTcount: A:0.08, C:0.02, G:0.06, T:0.85
Consensus pattern (25 bp):
TTTTATTTTGTTTTTTATTTTTTTC
Found at i:35861101 original size:20 final size:20
Alignment explanation
Indices: 35861073--35861110 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
35861063 TTTGTTTTTA
*
35861073 TTTTGTTTTTTTATTTTGTT
1 TTTTATTTTTTTATTTTGTT
*
35861093 TTTTATTTTTTTCTTTTG
1 TTTTATTTTTTTATTTTG
35861111 GTGCAGAACG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.05, C:0.03, G:0.08, T:0.84
Consensus pattern (20 bp):
TTTTATTTTTTTATTTTGTT
Found at i:35861102 original size:13 final size:12
Alignment explanation
Indices: 35861057--35861101 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
35861047 TATATATATA
35861057 TTTTATTTTG-T
1 TTTTATTTTGTT
35861068 TTTTATTTTGTTT
1 TTTTATTTTG-TT
35861081 TTTTATTTTGTT
1 TTTTATTTTGTT
35861093 TTTTATTTT
1 TTTTATTTT
35861102 TTTCTTTTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.31
12 11 0.34
13 11 0.34
ACGTcount: A:0.09, C:0.00, G:0.07, T:0.84
Consensus pattern (12 bp):
TTTTATTTTGTT
Found at i:35861109 original size:13 final size:12
Alignment explanation
Indices: 35861057--35861109 Score: 63
Period size: 12 Copynumber: 4.3 Consensus size: 12
35861047 TATATATATA
*
35861057 TTTTA-TTTTGT
1 TTTTATTTTTTT
35861068 TTTTATTTTGTTT
1 TTTTATTTT-TTT
*
35861081 TTTTATTTTGTT
1 TTTTATTTTTTT
35861093 TTTTATTTTTTT
1 TTTTATTTTTTT
35861105 CTTTT
1 -TTTT
35861110 GGTGCAGAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
11 5 0.14
12 16 0.44
13 15 0.42
ACGTcount: A:0.08, C:0.02, G:0.06, T:0.85
Consensus pattern (12 bp):
TTTTATTTTTTT
Found at i:35861708 original size:42 final size:42
Alignment explanation
Indices: 35861661--35861742 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
35861651 AATATGTGTG
* *
35861661 AAACGTTTAAAATTCAAACGTTTTAACTCTTGTTCCTATCCA
1 AAACGTTTAAAATTCAAACATTTGAACTCTTGTTCCTATCCA
* *
35861703 AAACGTTTGAAATTCAAACATTTGAACTCTTGTTCTTATC
1 AAACGTTTAAAATTCAAACATTTGAACTCTTGTTCCTATC
35861743 TTTTTGAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.39
Consensus pattern (42 bp):
AAACGTTTAAAATTCAAACATTTGAACTCTTGTTCCTATCCA
Found at i:35861977 original size:15 final size:15
Alignment explanation
Indices: 35861938--35861984 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
35861928 TGAGCTGGTG
*
35861938 GAGCTGAAATGGAGCT
1 GAGCTGAAAT-GAACT
*
35861954 -AGCTGGAAATGTACT
1 GAGCT-GAAATGAACT
35861969 GAGCTGAAATGAACT
1 GAGCTGAAATGAACT
35861984 G
1 G
35861985 GAAACAAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.34, C:0.13, G:0.32, T:0.21
Consensus pattern (15 bp):
GAGCTGAAATGAACT
Found at i:35863309 original size:25 final size:25
Alignment explanation
Indices: 35863272--35863367 Score: 85
Period size: 25 Copynumber: 3.9 Consensus size: 25
35863262 TCATTAGGGC
35863272 TACCGAT-TCTCAGCTCG-AGAGAGAT
1 TACCGATAT-TCAGCTCGTA-AGAGAT
*
35863297 TACCGATATTCAGCTCGTATGAGAT
1 TACCGATATTCAGCTCGTAAGAGAT
* *
35863322 T-CTCGATATTCAGCTCGTATGAGCT
1 TAC-CGATATTCAGCTCGTAAGAGAT
*
35863347 TACCG-T-TTACAGCTGGTAAGA
1 TACCGATATT-CAGCTCGTAAGA
35863368 ACATATCGAT
Statistics
Matches: 62, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
23 2 0.03
24 12 0.19
25 45 0.73
26 3 0.05
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (25 bp):
TACCGATATTCAGCTCGTAAGAGAT
Found at i:35866202 original size:15 final size:16
Alignment explanation
Indices: 35866182--35866211 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35866172 TGGTGCCTTG
35866182 TTGAT-ATGTGTTAAT
1 TTGATAATGTGTTAAT
35866197 TTGATAATGTGTTAA
1 TTGATAATGTGTTAA
35866212 AGCATGTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (16 bp):
TTGATAATGTGTTAAT
Found at i:35877235 original size:15 final size:14
Alignment explanation
Indices: 35877206--35877241 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
35877196 ATAAACTGAT
35877206 TTAAC-TAATAAAA
1 TTAACTTAATAAAA
35877219 TTAACTTAATCAAAA
1 TTAACTTAAT-AAAA
35877234 TTAACTTA
1 TTAACTTA
35877242 GTCGAATGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 5 0.24
14 4 0.19
15 12 0.57
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (14 bp):
TTAACTTAATAAAA
Found at i:35915498 original size:29 final size:29
Alignment explanation
Indices: 35915465--35915528 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
35915455 TAATCCACCA
35915465 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
35915494 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
35915524 CCCAA
1 CCCAA
35915529 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:35915502 original size:30 final size:30
Alignment explanation
Indices: 35915472--35915528 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
35915462 CCACCCAACT
35915472 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
35915501 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
35915529 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:35923848 original size:12 final size:12
Alignment explanation
Indices: 35923833--35923862 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
35923823 AAAATCCATC
35923833 TCATCCCCTTCT
1 TCATCCCCTTCT
*
35923845 TCATCTCCTTCT
1 TCATCCCCTTCT
35923857 TCATCC
1 TCATCC
35923863 TCACTATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.10, C:0.47, G:0.00, T:0.43
Consensus pattern (12 bp):
TCATCCCCTTCT
Found at i:35926303 original size:183 final size:183
Alignment explanation
Indices: 35926073--35926435 Score: 584
Period size: 184 Copynumber: 2.0 Consensus size: 183
35926063 ATATAATTAG
* * *
35926073 TACTTTAAATAAATAATATTATGATAAAACATAAATAAAATATTTTTGGGTTTTTATAATAAA-A
1 TACTTTAAATAAATAATAATACGATAAAACATAAATAAAAGATTTTTGGGTTTTTATAATAAAGA
* *
35926137 AAATAAAAATCGAGAAAATAAAGTGAACTTCAGGTGAATGAATTCTAACTTAATCAAATTTAAGC
66 AAATAAAAATAGAGAAAATAAAGTGAACTTCAGGTGAATGAATTCTAACTTAATCAAATCTAAGC
*
35926202 ATGGGTGATTAGCTCGCTTTGATGAGCATAACTAATTCATATTTTGGGTTTTAA
131 ATGGGAGATTAGCTCGCTTTGATGAGC-TAACTAATTCATATTTTGGGTTTTAA
*
35926256 TACTTTAAATAAATAATAATACGATAAAACATAAATATAAGATTTTTGGGTTTTTATAATAAAGA
1 TACTTTAAATAAATAATAATACGATAAAACATAAATAAAAGATTTTTGGGTTTTTATAATAAAGA
* * *
35926321 AAATAAAAATAGCGAAAATAAAGTGAACTTCGGGTGAATGAATTCTCACTTAATCAAATCTAAGC
66 AAATAAAAATAGAGAAAATAAAGTGAACTTCAGGTGAATGAATTCTAACTTAATCAAATCTAAGC
* * * *
35926386 ATGGGAGATTAGCTCGCTTTGGTGATCTCACTAATTCCTATTTTGGGTTT
131 ATGGGAGATTAGCTCGCTTTGATGAGCTAACTAATTCATATTTTGGGTTT
35926436 CCACTCAATC
Statistics
Matches: 165, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
183 80 0.48
184 85 0.52
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.35
Consensus pattern (183 bp):
TACTTTAAATAAATAATAATACGATAAAACATAAATAAAAGATTTTTGGGTTTTTATAATAAAGA
AAATAAAAATAGAGAAAATAAAGTGAACTTCAGGTGAATGAATTCTAACTTAATCAAATCTAAGC
ATGGGAGATTAGCTCGCTTTGATGAGCTAACTAATTCATATTTTGGGTTTTAA
Found at i:35926877 original size:21 final size:20
Alignment explanation
Indices: 35926847--35926885 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
35926837 CTGTCATTAT
*
35926847 TAAGTCTCTATTTCTGTGGC
1 TAAGTCTCTATTTATGTGGC
35926867 TAAGTACTCTATTTATGTG
1 TAAGT-CTCTATTTATGTG
35926886 TTTGAGATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.21, C:0.15, G:0.18, T:0.46
Consensus pattern (20 bp):
TAAGTCTCTATTTATGTGGC
Found at i:35927632 original size:13 final size:13
Alignment explanation
Indices: 35927614--35927639 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35927604 TTAGGTTTCA
35927614 AGATCATCTCTGG
1 AGATCATCTCTGG
35927627 AGATCATCTCTGG
1 AGATCATCTCTGG
35927640 TGCTTTTACG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (13 bp):
AGATCATCTCTGG
Found at i:35931439 original size:25 final size:25
Alignment explanation
Indices: 35931411--35931502 Score: 96
Period size: 25 Copynumber: 3.7 Consensus size: 25
35931401 AACTTTTCGA
35931411 TATTCAGCTCGCATGAGCTTCCTGT
1 TATTCAGCTCGCATGAGCTTCCTGT
* * *
35931436 TATTCAGCACACATGAGCTTCCCGT
1 TATTCAGCTCGCATGAGCTTCCTGT
* * * *
35931461 TATTCAGCTCGGAAGAGCTTACTAT
1 TATTCAGCTCGCATGAGCTTCCTGT
* *
35931486 T-TACAGCTCGTATGAGC
1 TATTCAGCTCGCATGAGC
35931503 ATACATGTAT
Statistics
Matches: 54, Mismatches: 13, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
24 13 0.24
25 41 0.76
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.32
Consensus pattern (25 bp):
TATTCAGCTCGCATGAGCTTCCTGT
Found at i:35932789 original size:16 final size:16
Alignment explanation
Indices: 35932763--35932804 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
35932753 ATTTCGATTG
35932763 GTTTTTTATATG-AAT
1 GTTTTTTATATGAAAT
35932778 GTTTTGTTATATGAAAT
1 GTTTT-TTATATGAAAT
35932795 GTTTATTTAT
1 GTTT-TTTAT
35932805 TTGATTTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 5 0.21
16 7 0.29
17 11 0.46
18 1 0.04
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (16 bp):
GTTTTTTATATGAAAT
Found at i:35934591 original size:36 final size:35
Alignment explanation
Indices: 35934551--35934628 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 35
35934541 AGAACATCGA
*
35934551 TAATCTAGCCAAAACACACGAGATGCTCATAAGAGC
1 TAATCTAGCCAAAACACACCA-ATGCTCATAAGAGC
* ** * *
35934587 TAATCCATTCGAAACACACCAATGCTCATAAGAGT
1 TAATCTAGCCAAAACACACCAATGCTCATAAGAGC
35934622 TAATCTA
1 TAATCTA
35934629 TTTGAAACAC
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
35 19 0.54
36 16 0.46
ACGTcount: A:0.41, C:0.24, G:0.13, T:0.22
Consensus pattern (35 bp):
TAATCTAGCCAAAACACACCAATGCTCATAAGAGC
Found at i:35934619 original size:35 final size:35
Alignment explanation
Indices: 35934562--35934643 Score: 119
Period size: 35 Copynumber: 2.3 Consensus size: 35
35934552 AATCTAGCCA
*
35934562 AAACACACGAGATGCTCATAAGAGCTAATCCATTCG
1 AAACACACCA-ATGCTCATAAGAGCTAATCCATTCG
* * *
35934598 AAACACACCAATGCTCATAAGAGTTAATCTATTTG
1 AAACACACCAATGCTCATAAGAGCTAATCCATTCG
35934633 AAACACACCAA
1 AAACACACCAA
35934644 AACAGAGAGT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 33 0.79
36 9 0.21
ACGTcount: A:0.43, C:0.24, G:0.12, T:0.21
Consensus pattern (35 bp):
AAACACACCAATGCTCATAAGAGCTAATCCATTCG
Found at i:35938254 original size:31 final size:31
Alignment explanation
Indices: 35938213--35938279 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
35938203 TACAAATTGA
* *
35938213 TCACTGAATTATTCGAA-AGTTTTCATTTAAG
1 TCACTAAATTATTCGAATA-TTTTCATATAAG
*
35938244 TCACTAAATTATTCGAATATTTTTATATAAG
1 TCACTAAATTATTCGAATATTTTCATATAAG
35938275 TCACT
1 TCACT
35938280 CGACTGCTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
31 31 0.97
32 1 0.03
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.43
Consensus pattern (31 bp):
TCACTAAATTATTCGAATATTTTCATATAAG
Found at i:35939912 original size:17 final size:17
Alignment explanation
Indices: 35939890--35939923 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
35939880 TTCGAAGTTG
35939890 ATCTTCTCAATAAAATT
1 ATCTTCTCAATAAAATT
*
35939907 ATCTTCTTAATAAAATT
1 ATCTTCTCAATAAAATT
35939924 GTCTCAAGGT
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:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (17 bp):
ATCTTCTCAATAAAATT
Found at i:35940270 original size:17 final size:16
Alignment explanation
Indices: 35940250--35940300 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
35940240 TTATTAAATG
35940250 TATATACATAATAAAAA
1 TATATA-ATAATAAAAA
*
35940267 TATATAAAAATTAAAAA
1 TATATAATAA-TAAAAA
*
35940284 TAAATATATAA-AAAAA
1 TATATA-ATAATAAAAA
35940300 T
1 T
35940301 TCATGAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 9 0.31
17 17 0.59
18 3 0.10
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (16 bp):
TATATAATAATAAAAA
Found at i:35940617 original size:25 final size:25
Alignment explanation
Indices: 35940587--35940646 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
35940577 ATTTGCAAAC
* *
35940587 AAAAAAATATTTTAATACCAAATTG
1 AAAAAAATATTATAATACCAAAATG
*
35940612 AGAAAAAA-ATTATAATACGAAAATG
1 A-AAAAAATATTATAATACCAAAATG
35940637 AAAAAAATAT
1 AAAAAAATAT
35940647 ATATTTCAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 6 0.20
25 18 0.60
26 6 0.20
ACGTcount: A:0.63, C:0.05, G:0.07, T:0.25
Consensus pattern (25 bp):
AAAAAAATATTATAATACCAAAATG
Found at i:35941892 original size:21 final size:20
Alignment explanation
Indices: 35941868--35941918 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 20
35941858 ATTCATAACA
*
35941868 TATTCAATTCTCATCACTTGC
1 TATTCAAATCTCAT-ACTTGC
35941889 TATTTCAAATCTCATACTTGC
1 TA-TTCAAATCTCATACTTGC
*
35941910 TATACAAAT
1 TATTCAAAT
35941919 AGTTTTTGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 6 0.22
21 10 0.37
22 11 0.41
ACGTcount: A:0.31, C:0.24, G:0.04, T:0.41
Consensus pattern (20 bp):
TATTCAAATCTCATACTTGC
Found at i:35941895 original size:22 final size:21
Alignment explanation
Indices: 35941870--35941912 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
35941860 TCATAACATA
*
35941870 TTCAATTCTCATCACTTGCTAT
1 TTCAAATCTCAT-ACTTGCTAT
35941892 TTCAAATCTCATACTTGCTAT
1 TTCAAATCTCATACTTGCTAT
35941913 ACAAATAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.26, C:0.26, G:0.05, T:0.44
Consensus pattern (21 bp):
TTCAAATCTCATACTTGCTAT
Found at i:35943111 original size:11 final size:11
Alignment explanation
Indices: 35943088--35943165 Score: 61
Period size: 11 Copynumber: 7.1 Consensus size: 11
35943078 ATTTTTCTCA
35943088 TTTTCTTTCCTT
1 TTTTCTTT-CTT
35943100 TTTTCTTTCTT
1 TTTTCTTTCTT
* *
35943111 TTTCCCTTC-T
1 TTTTCTTTCTT
* *
35943121 GTTTCGTTTGTT
1 TTTTC-TTTCTT
*
35943133 CTTTCTTTCTT
1 TTTTCTTTCTT
* *
35943144 TTCTATTTC-T
1 TTTTCTTTCTT
35943154 TTTTCTTTCTT
1 TTTTCTTTCTT
35943165 T
1 T
35943166 CTTTATTCAT
Statistics
Matches: 50, Mismatches: 13, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
10 12 0.24
11 25 0.50
12 13 0.26
ACGTcount: A:0.01, C:0.22, G:0.04, T:0.73
Consensus pattern (11 bp):
TTTTCTTTCTT
Found at i:35943146 original size:21 final size:21
Alignment explanation
Indices: 35943088--35943165 Score: 68
Period size: 22 Copynumber: 3.6 Consensus size: 21
35943078 ATTTTTCTCA
* *
35943088 TTTTCTTTCCTTTTTTCTTTCT
1 TTTTCTTT-CTTTTCTATTTCT
* * *
35943110 TTTTCCCTTCTGTTTC-GTTTGT
1 TTTT-CTTTCT-TTTCTATTTCT
35943132 TCTTTCTTTCTTTTCTATTTCT
1 T-TTTCTTTCTTTTCTATTTCT
35943154 TTTTCTTTCTTT
1 TTTTCTTTCTTT
35943166 CTTTATTCAT
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
21 15 0.33
22 21 0.47
23 9 0.20
ACGTcount: A:0.01, C:0.22, G:0.04, T:0.73
Consensus pattern (21 bp):
TTTTCTTTCTTTTCTATTTCT
Found at i:35943159 original size:25 final size:26
Alignment explanation
Indices: 35943099--35943169 Score: 83
Period size: 25 Copynumber: 2.7 Consensus size: 26
35943089 TTTCTTTCCT
*
35943099 TTTTTCTTTCTTT-TTCCCTTCTGTTTCG
1 TTTTTCTTTCTTTCTT---TTCTATTTCG
35943127 TTTGTTCTTTCTTTCTTTTCTATTTC-
1 TTT-TTCTTTCTTTCTTTTCTATTTCG
35943153 TTTTTCTTTCTTTCTTT
1 TTTTTCTTTCTTTCTTT
35943170 ATTCATTCAT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
25 14 0.35
26 3 0.08
27 8 0.20
28 3 0.08
29 10 0.25
30 2 0.05
ACGTcount: A:0.01, C:0.21, G:0.04, T:0.73
Consensus pattern (26 bp):
TTTTTCTTTCTTTCTTTTCTATTTCG
Found at i:35943168 original size:33 final size:33
Alignment explanation
Indices: 35943088--35943169 Score: 80
Period size: 33 Copynumber: 2.5 Consensus size: 33
35943078 ATTTTTCTCA
*
35943088 TTTTCTTTCCTTT-TTTCTTTCTTTTTCCCTTCT
1 TTTTCTTT-CTTTCTTTCTTTCTTTTTCACTTCT
* * *
35943121 GTTTCGTTT-GTTCTTTCTTTC-TTTTCTATTTCT
1 TTTTC-TTTCTTTCTTTCTTTCTTTTTC-ACTTCT
35943154 TTTTCTTTCTTTCTTT
1 TTTTCTTTCTTTCTTT
35943170 ATTCATTCAT
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
32 10 0.26
33 26 0.67
34 3 0.08
ACGTcount: A:0.01, C:0.22, G:0.04, T:0.73
Consensus pattern (33 bp):
TTTTCTTTCTTTCTTTCTTTCTTTTTCACTTCT
Found at i:35943184 original size:15 final size:15
Alignment explanation
Indices: 35943150--35943187 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
35943140 TCTTTTCTAT
* *
35943150 TTCTTT-TTCTTTCT
1 TTCTTTATTCATTCA
35943164 TTCTTTATTCATTCA
1 TTCTTTATTCATTCA
35943179 TTCTTTATT
1 TTCTTTATT
35943188 TGTTTTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.11, C:0.18, G:0.00, T:0.71
Consensus pattern (15 bp):
TTCTTTATTCATTCA
Done.