Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr13
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: 91551117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2824764 characters in sequence are not A, C, G, or T
File 129 of 276
Found at i:41690241 original size:24 final size:24
Alignment explanation
Indices: 41690212--41690260 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
41690202 CTCTTAAAGG
41690212 TATGAATAAATGTTATATTTAAAT
1 TATGAATAAATGTTATATTTAAAT
41690236 TATGAATAAATGTTATATTTAAAT
1 TATGAATAAATGTTATATTTAAAT
41690260 T
1 T
41690261 TATGTGTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (24 bp):
TATGAATAAATGTTATATTTAAAT
Found at i:41690452 original size:21 final size:23
Alignment explanation
Indices: 41690405--41690454 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 23
41690395 GAAATTGATA
*
41690405 TGAATATGTGATTATTACGAAATC
1 TGAATATGTGATTATTA-GAAAAC
*
41690429 TGAATATTTG-TTATT-GAAAAC
1 TGAATATGTGATTATTAGAAAAC
41690450 TGAAT
1 TGAAT
41690455 TGAATTGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 10 0.42
23 5 0.21
24 9 0.38
ACGTcount: A:0.38, C:0.06, G:0.16, T:0.40
Consensus pattern (23 bp):
TGAATATGTGATTATTAGAAAAC
Found at i:41691005 original size:23 final size:23
Alignment explanation
Indices: 41690954--41691008 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
41690944 AGCTTTGTCA
41690954 ATCAGGCACTTTATGTGACGTAT
1 ATCAGGCACTTTATGTGACGTAT
*
41690977 ACCAGGCACTTTATGT-ATCGTAT
1 ATCAGGCACTTTATGTGA-CGTAT
*
41691000 TTCAGGCAC
1 ATCAGGCAC
41691009 CTCGTGTGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 1 0.04
23 27 0.96
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (23 bp):
ATCAGGCACTTTATGTGACGTAT
Found at i:41691907 original size:22 final size:22
Alignment explanation
Indices: 41691879--41691947 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
41691869 TCTTTGATTA
*
41691879 TTAGCACATTAGTGCTCTCCGT
1 TTAGCACATTAGTGCTCTCTGT
*
41691901 TTAGCACATCT-GTGCTATCTGT
1 TTAGCACAT-TAGTGCTCTCTGT
* * *
41691923 ATAACACTTTAGTGCTCTCTGT
1 TTAGCACATTAGTGCTCTCTGT
41691945 TTA
1 TTA
41691948 ATAGTGCATA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
21 1 0.03
22 36 0.95
23 1 0.03
ACGTcount: A:0.20, C:0.23, G:0.16, T:0.41
Consensus pattern (22 bp):
TTAGCACATTAGTGCTCTCTGT
Found at i:41692900 original size:60 final size:59
Alignment explanation
Indices: 41692826--41692941 Score: 178
Period size: 60 Copynumber: 1.9 Consensus size: 59
41692816 CTCATTTCCC
* * *
41692826 TACAAACATAGAATTAAAATTTTGTTTTTAGTATCCAAATTCTTTTGGGTTCATAAGTA
1 TACAAACATAGAATTAAAATTTTATTTTTAGTACCCAAATTCTTTTGGGTCCATAAGTA
* *
41692885 NTACAAATATAGAATTAAAATTTTATTTTTGGTACCCAAATTCTTTTGGGTCCATAA
1 -TACAAACATAGAATTAAAATTTTATTTTTAGTACCCAAATTCTTTTGGGTCCATAA
41692942 ATATTAGTTC
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.41
Consensus pattern (59 bp):
TACAAACATAGAATTAAAATTTTATTTTTAGTACCCAAATTCTTTTGGGTCCATAAGTA
Found at i:41698797 original size:47 final size:46
Alignment explanation
Indices: 41698729--41699097 Score: 224
Period size: 47 Copynumber: 7.7 Consensus size: 46
41698719 TTTGTGTGCT
*
41698729 AGTGTAAGACATGTCTGGGACATGCACCGGCCACATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCC
* *
41698775 AGTGTAAGACCATGTCTGGGACATGGCATC-G--ACATTGAGACGAGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCACATT---ATGAGAGCC
* * *
41698823 AGTGTAAGACATGTTTGGGACATGCATCGGCCCCGAGATGTAAAAGATGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGG--CC-ACAT-T-----ATGAGAGCC
* *
41698878 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGA-GATGTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATTATG-AGAGCC
* * * * **
41698924 AATGTAAGACATGTCTGGGACATGCATCGGCTACATGAT--GTGTT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCC
* *
41698968 AGTGTAAGACCATGTCTGGGACATGGCATCGG-TACGGA-TACGTGAGAGTC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCAC--ATTA--TGAGAGCC
* *
41699018 AGTGTAAGACCATGTTTGGGACATGGCAT-TG--AC-TTAACGTGAGAGCC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCACATT-A--TGAGAGCC
41699065 AGTGTAAGACCATGTCTGGGACATGGCATCGGC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGC
41699098 ATTATACCCT
Statistics
Matches: 266, Mismatches: 27, Indels: 57
0.76 0.08 0.16
Matches are distributed among these distances:
44 9 0.03
45 23 0.09
46 63 0.24
47 69 0.26
48 24 0.09
49 1 0.00
50 31 0.12
52 3 0.01
53 4 0.02
55 39 0.15
ACGTcount: A:0.28, C:0.19, G:0.31, T:0.23
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCC
Found at i:41698899 original size:55 final size:55
Alignment explanation
Indices: 41698816--41698920 Score: 192
Period size: 55 Copynumber: 1.9 Consensus size: 55
41698806 ACATTGAGAC
*
41698816 GAGAGCTAGTGTAAGACATGTTTGGGACATGCATCGGCCCCGAGATGTAAAAGAT
1 GAGAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCCCGAGATGTAAAAGAT
*
41698871 GAGAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTAA
1 GAGAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCCCGAGATGTAA
41698921 GCCAATGTAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.30, C:0.17, G:0.31, T:0.22
Consensus pattern (55 bp):
GAGAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCCCGAGATGTAAAAGAT
Found at i:41698937 original size:101 final size:103
Alignment explanation
Indices: 41698766--41698954 Score: 276
Period size: 101 Copynumber: 1.9 Consensus size: 103
41698756 CGGCCACATT
* * *
41698766 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACATTGAGACGAGAGCTAGTGTAAG
1 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACATCGAGACGAGAGCCAATGTAAG
*
41698831 ACATGTTTGGGACATGCATCGGCCCCGAGATGTAAAAG
66 ACATGTCTGGGACATGCATCGGCCCCGAGATGTAAAAG
* * * *
41698869 ATGAGAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGATGTA-AGCCAATGTAA
1 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACATCGAGACG-AGAGCCAATGTAA
41698931 GACATGTCTGGGACATGCATCGGC
65 GACATGTCTGGGACATGCATCGGC
41698955 TACATGATGT
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
101 45 0.58
102 15 0.19
103 17 0.22
ACGTcount: A:0.29, C:0.19, G:0.31, T:0.21
Consensus pattern (103 bp):
ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACATCGAGACGAGAGCCAATGTAAG
ACATGTCTGGGACATGCATCGGCCCCGAGATGTAAAAG
Found at i:41698964 original size:46 final size:44
Alignment explanation
Indices: 41698880--41698999 Score: 145
Period size: 46 Copynumber: 2.6 Consensus size: 44
41698870 TGAGAGCTAG
41698880 TGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTAAGCCAA
1 TGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGT--GCCAA
** *
41698926 TGTAAGACATGTCTGGGACATGCATCGG-CTAC-ATGATGTGTTAG
1 TGTAAGACATGTCTGGGACATGCATCGGCCT-CGA-GATGTGCCAA
41698970 TGTAAGACCATGTCTGGGACATGGCATCGG
1 TGTAAGA-CATGTCTGGGACAT-GCATCGG
41699000 TACGGATACG
Statistics
Matches: 67, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
44 9 0.13
45 17 0.25
46 41 0.61
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (44 bp):
TGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTGCCAA
Found at i:41702355 original size:15 final size:15
Alignment explanation
Indices: 41702335--41702364 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
41702325 TTTAAGCAAA
41702335 TATGCCCAAGAATAT
1 TATGCCCAAGAATAT
41702350 TATGCCCAAGAATAT
1 TATGCCCAAGAATAT
41702365 GTGTCTACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (15 bp):
TATGCCCAAGAATAT
Found at i:41711173 original size:26 final size:27
Alignment explanation
Indices: 41711144--41711203 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
41711134 CCACATATAT
*
41711144 ATATCTGT-TCTGGTGGCCTAGCCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
* * * *
41711170 ATATTTGTATCTGGTGACTTCGTCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
41711197 ATATCTG
1 ATATCTG
41711204 GCAGCCTCGT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 7 0.26
27 20 0.74
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.37
Consensus pattern (27 bp):
ATATCTGTATCTGGTGACCTAGCCACA
Found at i:41720737 original size:19 final size:20
Alignment explanation
Indices: 41720713--41720750 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
41720703 GGTACCACCA
41720713 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
41720732 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
41720751 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:41721090 original size:93 final size:93
Alignment explanation
Indices: 41720980--41721150 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
41720970 GCCCCTAAGT
* * *
41720980 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAAAGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
41721045 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * *
41721073 GAACTCGGACTCAACTCAAAGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAAAGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
41721138 CGAGTTCGGATGC
66 CGAGTTCGGATGC
41721151 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAAAGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:41721147 original size:46 final size:46
Alignment explanation
Indices: 41720975--41721147 Score: 199
Period size: 46 Copynumber: 3.7 Consensus size: 46
41720965 AACCCGCCCC
* * * *
41720975 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
* * *
41721021 TAAATGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATCCA
* * *
41721069 TCA-CGAACTCGGACTCAACTCAAAGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
41721114 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
41721148 TGCTCAACCA
Statistics
Matches: 105, Mismatches: 15, Indels: 14
0.78 0.11 0.10
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 59 0.56
47 28 0.27
48 2 0.02
49 2 0.02
50 4 0.04
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
Found at i:41721604 original size:30 final size:30
Alignment explanation
Indices: 41721570--41721629 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
41721560 ATTTAATACG
41721570 AACTTTAAAAAAATTACACTTTTGCCCCTA
1 AACTTTAAAAAAATTACACTTTTGCCCCTA
*** *
41721600 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTAAAAAAATTACACTTTTGCCCCTA
41721630 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (30 bp):
AACTTTAAAAAAATTACACTTTTGCCCCTA
Found at i:41725407 original size:48 final size:48
Alignment explanation
Indices: 41725325--41725613 Score: 290
Period size: 48 Copynumber: 6.0 Consensus size: 48
41725315 GTACTAGGGT
* * * *
41725325 TATGTGAGCGAGTGTAAGACCATGTTTGGAACATGACATCGGCATTTA
1 TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATCTA
* * * *
41725373 TATGAGAGCTAGTGTAAGACCATGTATGGGACATGGCATCGGCCTCGA
1 TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATCTA
* * * * * * *
41725421 CATGTGAGCTAGTGTAAGACCATGTTTCGAACATGGAATTGACATTTA
1 TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATCTA
* * * * * * *
41725469 TATGAGGGCTAGTGTAGGACCATGTCTGGGACATGGCATCGACCTCGA
1 TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATCTA
* * *
41725517 CATGTGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCACCAATA
1 TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATC--TA
* * * * *
41725567 TATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCTTCAGCATCT
1 TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATCT
41725614 TACCCTTTTG
Statistics
Matches: 190, Mismatches: 49, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
48 151 0.79
50 39 0.21
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (48 bp):
TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATCTA
Found at i:41725490 original size:96 final size:96
Alignment explanation
Indices: 41725326--41725603 Score: 407
Period size: 96 Copynumber: 2.9 Consensus size: 96
41725316 TACTAGGGTT
* *
41725326 ATGTGAGCGAGTGTAAGACCATGTTTGGAACAT-GACATCGGCATTTATATGAGAGCTAGTGTAA
1 ATGTGAGCTAGTGTAAGACCATGTTTGGAACATGGA-ATCGACATTTATATGAGAGCTAGTGTAA
* *
41725390 GACCATGTATGGGACATGGCATCGGCCTCGAC
65 GACCATGTCTGGGACATGGCATCGACCTCGAC
* * * *
41725422 ATGTGAGCTAGTGTAAGACCATGTTTCGAACATGGAATTGACATTTATATGAGGGCTAGTGTAGG
1 ATGTGAGCTAGTGTAAGACCATGTTTGGAACATGGAATCGACATTTATATGAGAGCTAGTGTAAG
41725487 ACCATGTCTGGGACATGGCATCGACCTCGAC
66 ACCATGTCTGGGACATGGCATCGACCTCGAC
* * *
41725518 ATGTGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCACCA-ATATATGAGAGCCAGTGT
1 ATGTGAGCTAGTGTAAGACCATGTTTGGAACATGGAATC-G-A-CATTTATATGAGAGCTAGTGT
41725582 AAGACCATGTCTGGGACATGGC
63 AAGACCATGTCTGGGACATGGC
41725604 TTCAGCATCT
Statistics
Matches: 163, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
96 121 0.74
97 3 0.02
98 37 0.23
99 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (96 bp):
ATGTGAGCTAGTGTAAGACCATGTTTGGAACATGGAATCGACATTTATATGAGAGCTAGTGTAAG
ACCATGTCTGGGACATGGCATCGACCTCGAC
Found at i:41726687 original size:28 final size:28
Alignment explanation
Indices: 41726650--41726704 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
41726640 CACGGGCTGA
41726650 GACACAGGCGTGT-CATGGCCGTGTGAGG
1 GACACAGGCGTGTACA-GGCCGTGTGAGG
*
41726678 GACACGGGCGTGTACCAGGCCGTGTGA
1 GACACAGGCGTGTA-CAGGCCGTGTGA
41726705 AAACCCTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 12 0.50
29 10 0.42
30 2 0.08
ACGTcount: A:0.18, C:0.24, G:0.42, T:0.16
Consensus pattern (28 bp):
GACACAGGCGTGTACAGGCCGTGTGAGG
Found at i:41727512 original size:21 final size:22
Alignment explanation
Indices: 41727471--41727521 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 22
41727461 GGGCTCACAC
*
41727471 GCCCGTGTGGTCCAAGGGACAT
1 GCCCGTGTGGACCAAGGGACAT
*
41727493 GCCCGTGT-GACCATGGGACAT
1 GCCCGTGTGGACCAAGGGACAT
41727514 GCCCGTGT
1 GCCCGTGT
41727522 CACCCGAGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 19 0.70
22 8 0.30
ACGTcount: A:0.16, C:0.29, G:0.35, T:0.20
Consensus pattern (22 bp):
GCCCGTGTGGACCAAGGGACAT
Found at i:41727532 original size:21 final size:21
Alignment explanation
Indices: 41727486--41727541 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
41727476 TGTGGTCCAA
* *
41727486 GGGACATGCCCGTGTGACCAT
1 GGGACATGCCCGTGTCACCAC
41727507 GGGACATGCCCGTGTCACC-C
1 GGGACATGCCCGTGTCACCAC
*
41727527 GAGGACATGCTCGTG
1 G-GGACATGCCCGTG
41727542 CTACAGGTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.97
ACGTcount: A:0.18, C:0.30, G:0.34, T:0.18
Consensus pattern (21 bp):
GGGACATGCCCGTGTCACCAC
Found at i:41731341 original size:46 final size:46
Alignment explanation
Indices: 41731291--41731466 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
41731281 TGGTTGAGCA
* *
41731291 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
*** *
41731337 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GAA--
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAATG
41731384 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
41731430 -CTTGAGCACGTTGAGTTGAGTTCGAGTTCACTTATGG
1 TC-CGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
41731467 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 13, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
43 1 0.01
44 4 0.04
45 2 0.02
46 63 0.58
47 33 0.30
48 1 0.01
49 4 0.04
50 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.31
Consensus pattern (46 bp):
TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:41731449 original size:93 final size:93
Alignment explanation
Indices: 41731290--41731458 Score: 277
Period size: 93 Copynumber: 1.8 Consensus size: 93
41731280 ATGGTTGAGC
* *
41731290 ATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATGTCCGAGCTCGTTGAGTTG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAGCACGTTGAGTTG
41731355 AGTCCGAGTTCGAGAGATGTAACTAGGA
66 AGTCCGAGTTCGAGAGATGTAACTAGGA
* *
41731383 ATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG-CTTGAGCACGTTGAGTT
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC-CGAGCACGTTGAGTT
*
41731447 GAGTTCGAGTTC
65 GAGTCCGAGTTC
41731459 ACTTATGGGC
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 1 0.01
93 69 0.99
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.30
Consensus pattern (93 bp):
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAGCACGTTGAGTTG
AGTCCGAGTTCGAGAGATGTAACTAGGA
Found at i:41746390 original size:13 final size:13
Alignment explanation
Indices: 41746372--41746399 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
41746362 TTAGAAACGT
41746372 ATATTTTCAATGG
1 ATATTTTCAATGG
41746385 ATATTTTCAATGG
1 ATATTTTCAATGG
41746398 AT
1 AT
41746400 TTGATTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.46
Consensus pattern (13 bp):
ATATTTTCAATGG
Found at i:41747270 original size:24 final size:24
Alignment explanation
Indices: 41747233--41747309 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 24
41747223 ATGGTTGTTC
* *
41747233 AACCTTTCATCTTTCATCTCCTTT
1 AACCTTTAACCTTTCATCTCCTTT
* * *
41747257 GACCTTCT-ACCTTTTATCTTCTTT
1 AACCTT-TAACCTTTCATCTCCTTT
*
41747281 AACCTTTAACCTTTCATCTACTTGT
1 AACCTTTAACCTTTCATCTCCTT-T
41747306 AACC
1 AACC
41747310 CCTTTTTTCT
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
23 1 0.02
24 36 0.84
25 6 0.14
ACGTcount: A:0.19, C:0.31, G:0.03, T:0.47
Consensus pattern (24 bp):
AACCTTTAACCTTTCATCTCCTTT
Found at i:41749532 original size:16 final size:16
Alignment explanation
Indices: 41749511--41749548 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
41749501 TAAAAATAAT
41749511 ACATAAGACTACAAAA
1 ACATAAGACTACAAAA
* *
41749527 ACATAA-ACTTCTAAA
1 ACATAAGACTACAAAA
41749542 ACATAAG
1 ACATAAG
41749549 CTGTTTGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.58, C:0.18, G:0.05, T:0.18
Consensus pattern (16 bp):
ACATAAGACTACAAAA
Found at i:41752123 original size:16 final size:16
Alignment explanation
Indices: 41752102--41752132 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
41752092 AAACGAGGAA
41752102 GACCTTGCAACAGAAG
1 GACCTTGCAACAGAAG
41752118 GACCTTGCAACAGAA
1 GACCTTGCAACAGAA
41752133 AAGAAAGCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.13
Consensus pattern (16 bp):
GACCTTGCAACAGAAG
Found at i:41772710 original size:47 final size:47
Alignment explanation
Indices: 41772645--41772781 Score: 229
Period size: 47 Copynumber: 2.9 Consensus size: 47
41772635 GAAATGATAG
41772645 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGA
* ** *
41772692 TAAGGCCTAATGGCCGATGTGAAGAATGTGAAAGTGTATATACGTGG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGA
*
41772739 TAAGGCCTAATGGCCGATGTGATGAATATGAAAGTGTATATAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
41772782 GTNNNNNNNN
Statistics
Matches: 83, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 83 1.00
ACGTcount: A:0.34, C:0.09, G:0.28, T:0.28
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGA
Found at i:41772958 original size:47 final size:47
Alignment explanation
Indices: 41772879--41773164 Score: 396
Period size: 47 Copynumber: 6.1 Consensus size: 47
41772869 NNNNNNNNNN
41772879 TAAGGCCTATAATGGCCGATGTGATGAA--TGAAAGTGTATATATGTGA
1 TAAGGCC--TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
41772926 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
41772973 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
41773020 TAAGGCCTAATGGCTGATGTGATGAATGTGAAAGTGTATATAGGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * *
41773067 TAAGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATATATGTAA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * * *
41773114 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
41773161 TAAG
1 TAAG
41773165 TCCCAAGGGG
Statistics
Matches: 221, Mismatches: 16, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
45 19 0.09
47 202 0.91
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.28
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:41773339 original size:37 final size:36
Alignment explanation
Indices: 41773283--41773360 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 36
41773273 CCGAGCTCTA
* * *
41773283 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGT-CGGGT
* *
41773320 AAGACCCGATAACTTCGTGTGGAGATTATGTCTGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCGGGT
41773356 AAGAC
1 AAGAC
41773361 TTCGTAATAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
36 9 0.25
37 27 0.75
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (36 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCGGGT
Found at i:41779524 original size:50 final size:49
Alignment explanation
Indices: 41779361--41779597 Score: 269
Period size: 50 Copynumber: 4.8 Consensus size: 49
41779351 TGACGTCACG
*
41779361 TGTGTAGTACTAAGTACAGGCTACTACGTGTACCAGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
* * * * ** * * * *
41779410 TGTGTATTACCAAGTGTAGGCTACTATGCATACCCGATAACTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TT-GGTCGCA
* ** *
41779461 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCGCT
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT-GGTCGCA
*
41779511 TGTGTAGTACTAAGTGCAGGATACTACGTGTACCAGATAATTGGT-GCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
* * *
41779559 TGTGTAGTGCTAAGTGCAGGCTACTATGCGTACCAGATA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
41779598 GCTTTGGATA
Statistics
Matches: 152, Mismatches: 34, Indels: 5
0.80 0.18 0.03
Matches are distributed among these distances:
48 37 0.24
49 35 0.23
50 46 0.30
51 34 0.22
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.30
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
Found at i:41784831 original size:50 final size:49
Alignment explanation
Indices: 41784597--41784840 Score: 206
Period size: 50 Copynumber: 4.9 Consensus size: 49
41784587 CTATTGTGAC
*
41784597 GTCACGTGTGTAGTGCTAAGTGCAGGCTACTACGTGTACCAGATAATT-G
1 GTCAC-TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTAG
* * * * * * * * *
41784646 GTCGCATGTGCAGTAATAAGTGCAAGCAACTATGCGTACCCGATAACTTCG
1 GTCAC-TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TTAG
* * * **
41784697 ATCACGTGTGTAGTACTAAGTGCATGCTACTACGTGTATCAGATGGTTAG
1 GTCAC-TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTAG
* * *
41784747 GTCACGTTTGTAGTACTAAGTGCAGGATACTACGTGTACCGGATAATT-G
1 GTCAC-TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTAG
* * ***
41784796 GTGCA-TGTGTAGTGCTAAGTACAGGCTACTATACGTACCAGATAA
1 GT-CACTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA
41784841 CTTTGGCTGC
Statistics
Matches: 152, Mismatches: 40, Indels: 7
0.76 0.20 0.04
Matches are distributed among these distances:
48 32 0.21
49 39 0.26
50 47 0.31
51 34 0.22
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.28
Consensus pattern (49 bp):
GTCACTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTAG
Found at i:41787394 original size:13 final size:13
Alignment explanation
Indices: 41787376--41787402 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
41787366 GGCTCAGCAG
41787376 GACACGCCCGTGT
1 GACACGCCCGTGT
41787389 GACACGCCCGTGT
1 GACACGCCCGTGT
41787402 G
1 G
41787403 CGACTTCTTT
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:0.15, C:0.37, G:0.33, T:0.15
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:41797425 original size:31 final size:32
Alignment explanation
Indices: 41797387--41797446 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
41797377 CAATAATCTC
*
41797387 CATTACTTT-TGAACTAGTTTTCATTTTTGTT
1 CATTACTTTATCAACTAGTTTTCATTTTTGTT
**
41797418 CATTACTTTATCATTTAGTTTTCATTTTT
1 CATTACTTTATCAACTAGTTTTCATTTTT
41797447 AGGTTCTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 9 0.36
32 16 0.64
ACGTcount: A:0.20, C:0.13, G:0.07, T:0.60
Consensus pattern (32 bp):
CATTACTTTATCAACTAGTTTTCATTTTTGTT
Found at i:41813601 original size:40 final size:40
Alignment explanation
Indices: 41813565--41813695 Score: 181
Period size: 40 Copynumber: 3.3 Consensus size: 40
41813555 CAGCTATTTG
* *
41813565 TGGCACTTAGTGTGCGATTCGACATAACTTCGGCTATATA
1 TGGCACTTAGTGTGCGATTTGACATAGCTTCGGCTATATA
*
41813605 TGGCACTTAGTGTGCGATTTGATATAGCTTCGGCTATATA
1 TGGCACTTAGTGTGCGATTTGACATAGCTTCGGCTATATA
** * * * *
41813645 TGTTACTTAGTGTGTGATTTTAGATAGCTTCGGCTATGTA
1 TGGCACTTAGTGTGCGATTTGACATAGCTTCGGCTATATA
41813685 TGGCACTTAGT
1 TGGCACTTAGT
41813696 ATGCAAGATA
Statistics
Matches: 80, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 80 1.00
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.38
Consensus pattern (40 bp):
TGGCACTTAGTGTGCGATTTGACATAGCTTCGGCTATATA
Found at i:41814935 original size:33 final size:33
Alignment explanation
Indices: 41814802--41814933 Score: 121
Period size: 33 Copynumber: 4.2 Consensus size: 33
41814792 AATATGCAAA
* * *
41814802 ACAGTCTGTGCTTTAGCCCTATACAATATCAGT
1 ACAGTCTGGGCCTTAGCCCTATACAGTATCAGT
* * * * *
41814835 AAAGTCTGGGTCTTAGCCCTATATAGTAACAAT
1 ACAGTCTGGGCCTTAGCCCTATACAGTATCAGT
*
41814868 ACAATCTGGGCCTTAGCCCTATACAGTA--A-T
1 ACAGTCTGGGCCTTAGCCCTATACAGTATCAGT
* * *
41814898 --AGTGTGGGCCTAAGCCCGATACAGTATCAGT
1 ACAGTCTGGGCCTTAGCCCTATACAGTATCAGT
41814929 ACAGT
1 ACAGT
41814934 GTAATGCAAT
Statistics
Matches: 78, Mismatches: 16, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
28 22 0.28
30 2 0.03
31 2 0.03
33 52 0.67
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.28
Consensus pattern (33 bp):
ACAGTCTGGGCCTTAGCCCTATACAGTATCAGT
Found at i:41815363 original size:75 final size:74
Alignment explanation
Indices: 41815279--41815420 Score: 194
Period size: 74 Copynumber: 1.9 Consensus size: 74
41815269 GGGTATTATA
* * *
41815279 GTCATTTTACCCGATAGGGGCATTACGGTCATTTTATCCTACAGGGGCAGTACGATCATTTTACC
1 GTCATTTTACCCGACAAGGGCATTACGGTCA-TTTATCCTACAGGGACAGTACGATCATTTTACC
41815344 CTATATTACG
65 CTATATTACG
* * * * * *
41815354 GTCATTTTACCCTACAAGGGCGTTACGGTCATTTATTCTACAGGGACATTACGGTTATTTTACCC
1 GTCATTTTACCCGACAAGGGCATTACGGTCATTTATCCTACAGGGACAGTACGATCATTTTACCC
41815419 TA
66 TA
41815421 CAAGGGCATT
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
74 31 0.53
75 27 0.47
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.35
Consensus pattern (74 bp):
GTCATTTTACCCGACAAGGGCATTACGGTCATTTATCCTACAGGGACAGTACGATCATTTTACCC
TATATTACG
Found at i:41815395 original size:26 final size:27
Alignment explanation
Indices: 41815252--41815444 Score: 168
Period size: 27 Copynumber: 7.4 Consensus size: 27
41815242 GGGCATAATC
* * **
41815252 GTCATTTTACCATACAAGGGTATTATA
1 GTCATTTTACCCTACAAGGGCATTACG
* * *
41815279 GTCATTTTACCCGATAGGGGCATTACG
1 GTCATTTTACCCTACAAGGGCATTACG
* * *
41815306 GTCATTTTATCCTACAGGGGCAGTACG
1 GTCATTTTACCCTACAAGGGCATTACG
* *
41815333 ATCATTTTACCCT---A---TATTACG
1 GTCATTTTACCCTACAAGGGCATTACG
*
41815354 GTCATTTTACCCTACAAGGGCGTTACG
1 GTCATTTTACCCTACAAGGGCATTACG
**
41815381 GTCA-TTTATTCTAC-AGGGACATTACG
1 GTCATTTTACCCTACAAGGG-CATTACG
* *
41815407 GTTATTTTACCCTACAAGGGCATTATG
1 GTCATTTTACCCTACAAGGGCATTACG
41815434 GTCATTTTACC
1 GTCATTTTACC
41815445 TATTTTGAGG
Statistics
Matches: 130, Mismatches: 27, Indels: 18
0.74 0.15 0.10
Matches are distributed among these distances:
21 17 0.13
24 1 0.01
25 4 0.03
26 17 0.13
27 87 0.67
28 4 0.03
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCCTACAAGGGCATTACG
Found at i:41819724 original size:4 final size:4
Alignment explanation
Indices: 41819715--41819745 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
41819705 TTACTACTAA
41819715 TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
41819746 ATATATACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:41832214 original size:29 final size:29
Alignment explanation
Indices: 41832182--41832248 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
41832172 CATGGCCTTT
* *
41832182 TTAGGCCCAAATCACCTGTATATGGCCCA
1 TTAGGCCCAAATCACATGTATACGGCCCA
* * *
41832211 TTAGGCCTAAATCACATTTATACGGCCCG
1 TTAGGCCCAAATCACATGTATACGGCCCA
41832240 TTAGGCCCA
1 TTAGGCCCA
41832249 GTCACATTCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (29 bp):
TTAGGCCCAAATCACATGTATACGGCCCA
Found at i:41837706 original size:40 final size:40
Alignment explanation
Indices: 41837627--41837789 Score: 193
Period size: 40 Copynumber: 4.1 Consensus size: 40
41837617 CGGATGATAA
* * **
41837627 CCGGACTAAGATCCGAAGGCATTCGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGCTATAT
* * * *
41837667 CCGGGCTATGTCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGTTG-CTATAT
*
41837707 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGCTATAT
* * * *
41837747 CTGGGCTAAGACCCGAAGGCATTTGTACGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGCTATAT
41837787 CCG
1 CCG
41837790 ACTAAATCCC
Statistics
Matches: 104, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
39 2 0.02
40 100 0.96
41 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGCTATAT
Found at i:41837785 original size:80 final size:80
Alignment explanation
Indices: 41837627--41837803 Score: 234
Period size: 80 Copynumber: 2.2 Consensus size: 80
41837617 CGGATGATAA
* * *
41837627 CCGGACTAAGATCCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTATGTCCCGAAGGCATTTA
1 CCGGACTAAGACCCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTA
* *
41837692 TGCTAGTGATTATAT
66 TACGAGTGATTATAT
* * * *
41837707 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCTGGGCTAAGACCCGAAGGCATTTG
1 CCGGACTAAGACCCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTA
41837772 TACGAGTTG-TTATAT
66 TACGAG-TGATTATAT
41837787 CC-GACTAA-ATCCCGAAG
1 CCGGACTAAGA-CCCGAAG
41837804 ATACTTGGGT
Statistics
Matches: 85, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
78 1 0.01
79 12 0.14
80 70 0.82
81 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.27
Consensus pattern (80 bp):
CCGGACTAAGACCCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTA
TACGAGTGATTATAT
Found at i:41838071 original size:22 final size:22
Alignment explanation
Indices: 41838031--41838072 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
41838021 GAATGTGCAT
*
41838031 ATATGAAGTTATTCATTTAGCC
1 ATATGAAGTTATACATTTAGCC
41838053 ATATGAATGTTATAC-TTTAG
1 ATATGAA-GTTATACATTTAG
41838073 TCAAAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (22 bp):
ATATGAAGTTATACATTTAGCC
Found at i:41845614 original size:30 final size:29
Alignment explanation
Indices: 41845546--41845634 Score: 94
Period size: 29 Copynumber: 3.1 Consensus size: 29
41845536 AAATTCACAT
*
41845546 ACCTATATCTGGCCCATTAAGCCC-AATC
1 ACCTATATATGGCCCATTAAGCCCAAATC
*
41845574 A--TATTCATATGGCCTCTTTAAGCCCAAATC
1 ACCTA-T-ATATGGCC-CATTAAGCCCAAATC
* *
41845604 ACCTATATATGCCCCATTAGGCCCAAATC
1 ACCTATATATGGCCCATTAAGCCCAAATC
41845633 AC
1 AC
41845635 ATTTATACAG
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
26 2 0.04
27 1 0.02
28 8 0.16
29 24 0.48
30 12 0.24
31 1 0.02
32 2 0.04
ACGTcount: A:0.30, C:0.33, G:0.10, T:0.27
Consensus pattern (29 bp):
ACCTATATATGGCCCATTAAGCCCAAATC
Found at i:41845907 original size:16 final size:16
Alignment explanation
Indices: 41845886--41845932 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
41845876 CAAACTTTCA
41845886 GCTTTTCGGCATTTTG
1 GCTTTTCGGCATTTTG
* *
41845902 GCTTTTCGGTATTTCG
1 GCTTTTCGGCATTTTG
*
41845918 GCATTTCGGC-TTTTG
1 GCTTTTCGGCATTTTG
41845933 TCAATTCATA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
15 4 0.15
16 22 0.85
ACGTcount: A:0.06, C:0.19, G:0.26, T:0.49
Consensus pattern (16 bp):
GCTTTTCGGCATTTTG
Found at i:41845918 original size:8 final size:8
Alignment explanation
Indices: 41845889--41845927 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
41845879 ACTTTCAGCT
41845889 TTTCGGCA
1 TTTCGGCA
* *
41845897 TTTTGGCT
1 TTTCGGCA
*
41845905 TTTCGGTA
1 TTTCGGCA
41845913 TTTCGGCA
1 TTTCGGCA
41845921 TTTCGGC
1 TTTCGGC
41845928 TTTTGTCAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.08, C:0.21, G:0.26, T:0.46
Consensus pattern (8 bp):
TTTCGGCA
Found at i:41851323 original size:13 final size:13
Alignment explanation
Indices: 41851305--41851330 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41851295 TCGACAGGGA
41851305 CACGCCCGTGTGG
1 CACGCCCGTGTGG
41851318 CACGCCCGTGTGG
1 CACGCCCGTGTGG
41851331 GGTGGCTTAG
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:0.08, C:0.38, G:0.38, T:0.15
Consensus pattern (13 bp):
CACGCCCGTGTGG
Found at i:41852836 original size:13 final size:15
Alignment explanation
Indices: 41852807--41852838 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
41852797 GAAAAAGGCT
41852807 GATTCAGAGGCAAGA
1 GATTCAGAGGCAAGA
41852822 GATTCA-AGG-AAGA
1 GATTCAGAGGCAAGA
41852835 GATT
1 GATT
41852839 GATGAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 3 0.18
15 6 0.35
ACGTcount: A:0.41, C:0.09, G:0.31, T:0.19
Consensus pattern (15 bp):
GATTCAGAGGCAAGA
Found at i:41864504 original size:40 final size:40
Alignment explanation
Indices: 41864405--41864518 Score: 147
Period size: 40 Copynumber: 2.9 Consensus size: 40
41864395 GCGATTCAAT
* * * *
41864405 ATAGCTTCGGCTATATAAGCCACTTAGTATGCGATTTGAG
1 ATAGCTTCGGCTATATATGGCACTTAGTGTGTGATTTGAG
**
41864445 ATAGCTTCAACTATATATGGCACTTAGTGTGTGATTTGAG
1 ATAGCTTCGGCTATATATGGCACTTAGTGTGTGATTTGAG
* * *
41864485 ATAGCTTCGGCTATGTATGGCACCTAGCGTGTGA
1 ATAGCTTCGGCTATATATGGCACTTAGTGTGTGA
41864519 GATATCGAGT
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 63 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (40 bp):
ATAGCTTCGGCTATATATGGCACTTAGTGTGTGATTTGAG
Found at i:41864556 original size:28 final size:28
Alignment explanation
Indices: 41864499--41864558 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
41864489 CTTCGGCTAT
*
41864499 GTATGGCACCTAGCGTGTGAGATATCGA
1 GTATGGCACCTAGCGTGTGAGACATCGA
* * * *
41864527 GTATGGCACTTAGTGTGTGAGGCATTGA
1 GTATGGCACCTAGCGTGTGAGACATCGA
41864555 GTAT
1 GTAT
41864559 TCAACAACAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.23, C:0.13, G:0.33, T:0.30
Consensus pattern (28 bp):
GTATGGCACCTAGCGTGTGAGACATCGA
Found at i:41873914 original size:40 final size:40
Alignment explanation
Indices: 41873877--41874821 Score: 1682
Period size: 40 Copynumber: 23.6 Consensus size: 40
41873867 GCTACTCGTT
* *
41873877 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
41873917 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
41873957 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
41873997 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
41874037 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
41874077 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
41874117 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
41874157 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
41874197 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
41874237 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
41874277 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
41874317 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
41874357 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
41874397 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
41874437 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
41874477 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
41874517 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
41874557 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
41874597 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
41874637 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
41874677 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * * * * *
41874717 CCAATGTCTTCGGG-CTTAGCCCGAAATTAGTATCTCGTA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
41874756 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
* *
41874797 CAAA-ACCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
41874822 CATCATTCGA
Statistics
Matches: 878, Mismatches: 22, Indels: 10
0.96 0.02 0.01
Matches are distributed among these distances:
38 2 0.00
39 29 0.03
40 835 0.95
41 12 0.01
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:41876019 original size:56 final size:56
Alignment explanation
Indices: 41875952--41876071 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
41875942 TATTAGTTTA
41875952 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
41876008 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
41876064 TTGCCCAT
1 TTGCCCAT
41876072 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:41880715 original size:40 final size:40
Alignment explanation
Indices: 41880368--41880713 Score: 520
Period size: 40 Copynumber: 8.7 Consensus size: 40
41880358 GCTACTCGTT
* *
41880368 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
*
41880408 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
41880448 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
41880488 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
41880528 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
41880568 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
41880608 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
41880647 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
41880688 CAAA-GCCTTCGGGACTTAGCCCGGAT
1 CAAATGCCTTCGGGACTTAACCCGGAT
41880714 ATCATTCAAA
Statistics
Matches: 286, Mismatches: 15, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
38 2 0.01
39 33 0.12
40 238 0.83
41 13 0.05
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:41904317 original size:49 final size:49
Alignment explanation
Indices: 41904245--41904342 Score: 178
Period size: 49 Copynumber: 2.0 Consensus size: 49
41904235 TCATACAGCC
*
41904245 AATAACACACCAGTTTGAGGACAAGCCACCGGTAATGTAGATAAACTAT
1 AATAACACACCAGTTTGAGGACAAGCCACCAGTAATGTAGATAAACTAT
*
41904294 AATAACACACCAGTTTGTGGACAAGCCACCAGTAATGTAGATAAACTAT
1 AATAACACACCAGTTTGAGGACAAGCCACCAGTAATGTAGATAAACTAT
41904343 CAAAATTGTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.21
Consensus pattern (49 bp):
AATAACACACCAGTTTGAGGACAAGCCACCAGTAATGTAGATAAACTAT
Found at i:41904412 original size:20 final size:20
Alignment explanation
Indices: 41904387--41904441 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
41904377 ACCTGCTAGT
41904387 ATTGTAGACAAGCTACCAGA
1 ATTGTAGACAAGCTACCAGA
*
41904407 ATTGTAGACAAGCCACCAGA
1 ATTGTAGACAAGCTACCAGA
* *
41904427 ATTGCACACAAGCTA
1 ATTGTAGACAAGCTA
41904442 TCGATACTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.18
Consensus pattern (20 bp):
ATTGTAGACAAGCTACCAGA
Found at i:41906395 original size:17 final size:17
Alignment explanation
Indices: 41906369--41906402 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
41906359 TATATAATTG
*
41906369 AAATATGTTATAATATA
1 AAATAAGTTATAATATA
41906386 AAATAAGTTATAATATA
1 AAATAAGTTATAATATA
41906403 TTAAGTGGGG
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:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (17 bp):
AAATAAGTTATAATATA
Found at i:41907641 original size:24 final size:24
Alignment explanation
Indices: 41907579--41907661 Score: 94
Period size: 24 Copynumber: 3.5 Consensus size: 24
41907569 GAAATGATTT
* *
41907579 TGGCACTATGTGTACGAATTTGAA
1 TGGCACTATGTGTGCGGATTTGAA
* * *
41907603 TGGCATTATGAGTGCGGATTTGTA
1 TGGCACTATGTGTGCGGATTTGAA
*
41907627 TGGCACTATGTGTGCGGATTGGAA
1 TGGCACTATGTGTGCGGATTTGAA
* *
41907651 TGTCAATATGT
1 TGGCACTATGT
41907662 ATGTGAATTA
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.24, C:0.11, G:0.30, T:0.35
Consensus pattern (24 bp):
TGGCACTATGTGTGCGGATTTGAA
Found at i:41908417 original size:39 final size:39
Alignment explanation
Indices: 41908305--41908456 Score: 205
Period size: 39 Copynumber: 3.9 Consensus size: 39
41908295 ATTTGATGTA
*
41908305 TATCCGGACTTAAGGTCCGCAGGCTTCGTGCTGGAATTG
1 TATCCGGACTTAAGATCCGCAGGCTTCGTGCTGGAATTG
* *
41908344 TATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGAATTG
1 TATCCGGACTT-AAGATCCGCAGGCTTCGTGCTGGAATTG
* * * *
41908384 TATCCGGACTTAAGATCTGCAGGCTTCGTGCTGGTACTA
1 TATCCGGACTTAAGATCCGCAGGCTTCGTGCTGGAATTG
* * *
41908423 TATCCGGACTTAAGGTCTGCAGGCTTCGTACTGG
1 TATCCGGACTTAAGATCCGCAGGCTTCGTGCTGG
41908457 TACTATATCC
Statistics
Matches: 101, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
39 65 0.64
40 36 0.36
ACGTcount: A:0.19, C:0.24, G:0.29, T:0.28
Consensus pattern (39 bp):
TATCCGGACTTAAGATCCGCAGGCTTCGTGCTGGAATTG
Found at i:41912481 original size:43 final size:43
Alignment explanation
Indices: 41912419--41912503 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 43
41912409 TTGTGATTCT
* **
41912419 GATATGTGTTTACGAGTAAGACCTTGTCTGGGACAG-TGGCATC
1 GATATGTGGTTACGAGTAAGACCACGTCTGGGAC-GTTGGCATC
41912462 GATATGTGGTTAC-ATGTAAGACCACGTCTGGGACGTTGGCAT
1 GATATGTGGTTACGA-GTAAGACCACGTCTGGGACGTTGGCAT
41912504 TGTACGATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 2 0.05
43 35 0.95
ACGTcount: A:0.24, C:0.16, G:0.31, T:0.29
Consensus pattern (43 bp):
GATATGTGGTTACGAGTAAGACCACGTCTGGGACGTTGGCATC
Found at i:41918359 original size:17 final size:15
Alignment explanation
Indices: 41918325--41918373 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
41918315 AAGAAGTCTG
41918325 AGATAAAGAAATCCA
1 AGATAAAGAAATCCA
41918340 AGATAAAGAAACTCCCA
1 AGATAAAGAAA-T-CCA
**
41918357 AGATTCAGAAATCCA
1 AGATAAAGAAATCCA
41918372 AG
1 AG
41918374 TTACAATACC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 16 0.53
16 2 0.07
17 12 0.40
ACGTcount: A:0.53, C:0.18, G:0.14, T:0.14
Consensus pattern (15 bp):
AGATAAAGAAATCCA
Found at i:41925274 original size:45 final size:45
Alignment explanation
Indices: 41925210--41925376 Score: 253
Period size: 45 Copynumber: 3.7 Consensus size: 45
41925200 TAGGATTTCG
* * * *
41925210 ATATGTGTTTTCATGTAAGACAACGTCTGGGACTTTGGCATCAAT
1 ATATGTGTTTTCGTGTAAGACCACGTCTGGGACATTGGCATCGAT
*
41925255 ATATGTGTTTTCGTGTAAGACCACGTCTGGGACATTGGCATCGTT
1 ATATGTGTTTTCGTGTAAGACCACGTCTGGGACATTGGCATCGAT
* * *
41925300 ATATGTGTTTTCGTGTAAGACCACGTCTAGGACGTTGGCATTGAT
1 ATATGTGTTTTCGTGTAAGACCACGTCTGGGACATTGGCATCGAT
*
41925345 ATATGTGTTTTTGTGTAAGACCACGTCTGGGA
1 ATATGTGTTTTCGTGTAAGACCACGTCTGGGA
41925377 TGTTAACATT
Statistics
Matches: 111, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 111 1.00
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.36
Consensus pattern (45 bp):
ATATGTGTTTTCGTGTAAGACCACGTCTGGGACATTGGCATCGAT
Found at i:41925408 original size:45 final size:45
Alignment explanation
Indices: 41925210--41925396 Score: 248
Period size: 45 Copynumber: 4.2 Consensus size: 45
41925200 TAGGATTTCG
* * *
41925210 ATATGTGTTTTCATGTAAGACAACGTCTGGGACTTTGGCATCAAT
1 ATATGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCAAT
* **
41925255 ATATGTGTTTTCGTGTAAGACCACGTCTGGGACATTGGCATCGTT
1 ATATGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCAAT
* **
41925300 ATATGTGTTTTCGTGTAAGACCACGTCTAGGACGTTGGCATTGAT
1 ATATGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCAAT
* * ** *
41925345 ATATGTGTTTTTGTGTAAGACCACGTCTGGGATGTTAACATTAAT
1 ATATGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCAAT
41925390 ATATGTG
1 ATATGTG
41925397 GTTATGTGTA
Statistics
Matches: 127, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 127 1.00
ACGTcount: A:0.24, C:0.14, G:0.25, T:0.37
Consensus pattern (45 bp):
ATATGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCAAT
Found at i:41927187 original size:27 final size:27
Alignment explanation
Indices: 41927157--41927255 Score: 87
Period size: 27 Copynumber: 3.7 Consensus size: 27
41927147 TGTAGCATAG
**
41927157 AATTACCAAAATACCAC-TGGTTTG-AGA
1 AATTACCAAAATACC-CTTAATTTGTA-A
*
41927184 AATTACCGAAATACCCTTAATTTGTAA
1 AATTACCAAAATACCCTTAATTTGTAA
* **
41927211 AATTACCAAAATACCCCTAATTTACAA
1 AATTACCAAAATACCCTTAATTTGTAA
*
41927238 AATTA-TAGAAATACCCTT
1 AATTACCA-AAATACCCTT
41927256 GACTTTTTTA
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
26 2 0.03
27 57 0.95
28 1 0.02
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.29
Consensus pattern (27 bp):
AATTACCAAAATACCCTTAATTTGTAA
Found at i:41927423 original size:27 final size:26
Alignment explanation
Indices: 41927334--41927423 Score: 67
Period size: 27 Copynumber: 3.3 Consensus size: 26
41927324 TTACCAAAAC
***
41927334 ACCCTTGTAGGATGAAATGACTAAAAT
1 ACCCTTGTAGGAT-AAATGACCGTAAT
* *
41927361 ACCCTTAATAGG-TAAAAAGACCGTAA-
1 ACCCTT-GTAGGAT-AAATGACCGTAAT
*
41927387 AGCCCCTGTAGGATAAAGTGACCGTAAT
1 A-CCCTTGTAGGATAAA-TGACCGTAAT
41927415 ACCCTTGTA
1 ACCCTTGTA
41927424 TGGTAAAATG
Statistics
Matches: 48, Mismatches: 10, Indels: 10
0.71 0.15 0.15
Matches are distributed among these distances:
26 8 0.17
27 35 0.73
28 5 0.10
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (26 bp):
ACCCTTGTAGGATAAATGACCGTAAT
Found at i:41928273 original size:25 final size:24
Alignment explanation
Indices: 41928239--41928308 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 24
41928229 AGGAAGTGCT
41928239 AAAAGGGCTCTGCCCCAGTTTACC
1 AAAAGGGCTCTGCCCCAGTTTACC
*
41928263 GAAAAGGGCTCTGCCCCAGTTTATC
1 -AAAAGGGCTCTGCCCCAGTTTACC
*
41928288 AGAAAGGGCTTTGCCCCAGTT
1 A-AAAGGGCTCTGCCCCAGTT
41928309 ATTAAAAGAG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
24 1 0.02
25 41 0.98
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.23
Consensus pattern (24 bp):
AAAAGGGCTCTGCCCCAGTTTACC
Found at i:41928321 original size:24 final size:24
Alignment explanation
Indices: 41928238--41928321 Score: 98
Period size: 25 Copynumber: 3.4 Consensus size: 24
41928228 GAGGAAGTGC
*
41928238 TAAAAGGGCTCTGCCCCAGTTTACC
1 TAAAAGGGCTCTGCCCCAGTTTA-T
*
41928263 GAAAAGGGCTCTGCCCCAGTTTAT
1 TAAAAGGGCTCTGCCCCAGTTTAT
* *
41928287 CAGAAAGGGCTTTGCCCCAG-TTAT
1 TA-AAAGGGCTCTGCCCCAGTTTAT
41928311 TAAAAGAGGCT
1 TAAAAG-GGCT
41928322 AGGCCTCCAG
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
23 4 0.08
24 10 0.19
25 38 0.73
ACGTcount: A:0.27, C:0.25, G:0.24, T:0.24
Consensus pattern (24 bp):
TAAAAGGGCTCTGCCCCAGTTTAT
Found at i:41928515 original size:42 final size:42
Alignment explanation
Indices: 41928456--41928547 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 42
41928446 TAGTCTCCCC
* * ** **
41928456 AAATGGGCTTGCATACATTCATTGGTATTTTATGTGATATTG
1 AAATGGGCTTACATACATCCATTGACATTACATGTGATATTG
41928498 AAATGGGCTTACATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTACATACATCCATTGACATTACATGTGATATTG
41928540 AAATGGGC
1 AAATGGGC
41928548 CTAAGGGCCA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (42 bp):
AAATGGGCTTACATACATCCATTGACATTACATGTGATATTG
Found at i:41937350 original size:63 final size:63
Alignment explanation
Indices: 41937251--41937378 Score: 247
Period size: 63 Copynumber: 2.0 Consensus size: 63
41937241 CATAACTTTC
*
41937251 ATTTAGTATAATCTTTATTTATTTAAGTTTATCTTTAAATAATTTAACATCAATTCACTAAAA
1 ATTTAGTATAATCTTTATTTATTTAAGTTTATCTTTAAACAATTTAACATCAATTCACTAAAA
41937314 ATTTAGTATAATCTTTATTTATTTAAGTTTATCTTTAAACAATTTAACATCAATTCACTAAAA
1 ATTTAGTATAATCTTTATTTATTTAAGTTTATCTTTAAACAATTTAACATCAATTCACTAAAA
41937377 AT
1 AT
41937379 AAAATTTTAT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (63 bp):
ATTTAGTATAATCTTTATTTATTTAAGTTTATCTTTAAACAATTTAACATCAATTCACTAAAA
Found at i:41937536 original size:18 final size:18
Alignment explanation
Indices: 41937502--41937539 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
41937492 ATCAAACTAT
*
41937502 TATTTTAATATTTTTACA
1 TATTTAAATATTTTTACA
41937520 TATTTAAAT-TTTATTACA
1 TATTTAAATATTT-TTACA
41937538 TA
1 TA
41937540 AATTGGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (18 bp):
TATTTAAATATTTTTACA
Found at i:41938882 original size:3 final size:3
Alignment explanation
Indices: 41938874--41938898 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
41938864 GTTCAGTTTT
41938874 TGG TGG TGG TGG TGG TGG TGG TGG T
1 TGG TGG TGG TGG TGG TGG TGG TGG T
41938899 TGAACCTGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.64, T:0.36
Consensus pattern (3 bp):
TGG
Found at i:41940304 original size:25 final size:25
Alignment explanation
Indices: 41940270--41940317 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
41940260 CTCTCGTTGC
41940270 ACGAAAGTTTTGTTTATTAAAATTA
1 ACGAAAGTTTTGTTTATTAAAATTA
41940295 ACGAAAGTTTTGTTTATTAAAAT
1 ACGAAAGTTTTGTTTATTAAAAT
41940318 GCATAATTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.44
Consensus pattern (25 bp):
ACGAAAGTTTTGTTTATTAAAATTA
Found at i:41940452 original size:13 final size:13
Alignment explanation
Indices: 41940434--41940459 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41940424 TTTAGGGTGC
41940434 ATACACCAGTTTA
1 ATACACCAGTTTA
41940447 ATACACCAGTTTA
1 ATACACCAGTTTA
41940460 TTTTATTCAA
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:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (13 bp):
ATACACCAGTTTA
Found at i:41942686 original size:16 final size:16
Alignment explanation
Indices: 41942661--41942691 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41942651 CCTCTCACTT
*
41942661 TAATATTATTTTAATA
1 TAATACTATTTTAATA
41942677 TAATACTATTTTAAT
1 TAATACTATTTTAAT
41942692 TAAGATTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
TAATACTATTTTAATA
Found at i:41942689 original size:27 final size:27
Alignment explanation
Indices: 41942659--41942727 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 27
41942649 TACCTCTCAC
*
41942659 TTTAATATTATTTTAATATAATACT-AT
1 TTTAATATTATTTTAATATAACA-TAAT
* *
41942686 TTTAAT-TAAGATTTAATATAACATAAT
1 TTTAATATTA-TTTTAATATAACATAAT
41942713 TTTAATATATATTTT
1 TTTAATAT-TATTTT
41942728 TTATACATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
26 3 0.09
27 25 0.76
28 4 0.12
29 1 0.03
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (27 bp):
TTTAATATTATTTTAATATAACATAAT
Found at i:41946090 original size:13 final size:13
Alignment explanation
Indices: 41946072--41946097 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41946062 TTAGTCAGAT
41946072 TAGGACTTATAAA
1 TAGGACTTATAAA
41946085 TAGGACTTATAAA
1 TAGGACTTATAAA
41946098 CTTCTCATTT
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:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (13 bp):
TAGGACTTATAAA
Found at i:41960241 original size:42 final size:42
Alignment explanation
Indices: 41960182--41960265 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
41960172 CATCATGCTA
41960182 CACTCTATCAGATATTTAGAGGAATTCAAGACATAACTCTTT
1 CACTCTATCAGATATTTAGAGGAATTCAAGACATAACTCTTT
*
41960224 CACTCTTTCAGATATTTAGAGGAATTCAAGACATAACTCTTT
1 CACTCTATCAGATATTTAGAGGAATTCAAGACATAACTCTTT
41960266 TAATCTTATA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.35
Consensus pattern (42 bp):
CACTCTATCAGATATTTAGAGGAATTCAAGACATAACTCTTT
Found at i:41966071 original size:27 final size:27
Alignment explanation
Indices: 41966040--41967147 Score: 1313
Period size: 27 Copynumber: 40.6 Consensus size: 27
41966030 TTTAGTTCAC
* *
41966040 AAAATTACCAAAATACCCCTGATTTGT
1 AAAATTACCAAAATACCCTTGGTTTGT
* *
41966067 AAAATTACTAAAATACCCTTGGTTTAT
1 AAAATTACCAAAATACCCTTGGTTTGT
* * *
41966094 AAAATCATCAAAATACCCCTGGTTTGT
1 AAAATTACCAAAATACCCTTGGTTTGT
* *
41966121 AAAATTACTAAAATACCCTTGGTTTAT
1 AAAATTACCAAAATACCCTTGGTTTGT
* *
41966148 AAAATCACCAAAATACCCCTGGTTTGT
1 AAAATTACCAAAATACCCTTGGTTTGT
* * **
41966175 AAAATTACCAAAATACCATTAGTTTAC
1 AAAATTACCAAAATACCCTTGGTTTGT
41966202 AAAATTACCAAAATACCCTTGGTTTGT
1 AAAATTACCAAAATACCCTTGGTTTGT
* * *
41966229 AAAATTACTAAAATACCATTGGTTTAT
1 AAAATTACCAAAATACCCTTGGTTTGT
* *
41966256 AAAATCACCAAAATACCCTTAGTTTGT
1 AAAATTACCAAAATACCCTTGGTTTGT
**
41966283 AAAATTACCAAAATACCCTTGGTTTAC
1 AAAATTACCAAAATACCCTTGGTTTGT
*
41966310 AAAATTACCAAAATACCCTTAGTTTGT
1 AAAATTACCAAAATACCCTTGGTTTGT
* *
41966337 AAAATTACCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCTTGGTTTGT
41966364 AAAATTACCAAAATACCAC-TGGTTTGT
1 AAAATTACCAAAATACC-CTTGGTTTGT
* *
41966391 AAAATTACCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCTTGGTTTGT
* *
41966418 AAAATTACCAAAATACCCCTGATTTGT
1 AAAATTACCAAAATACCCTTGGTTTGT
* * * *
41966445 GAATTAGTTTGTAAAATTACTAAAATACCATTGGTTTAT
1 -AA--A--AT-T---AC--C-AAAATACCCTTGGTTTGT
41966484 AAAATTACCAAAATACCCCTT-GTTTGT
1 AAAATTACCAAAATA-CCCTTGGTTTGT
**
41966511 AAAATTACCAAAATACCCTTGGTTTAC
1 AAAATTACCAAAATACCCTTGGTTTGT
41966538 AAAATTACCAAAATACCCTTGGTTTGT
1 AAAATTACCAAAATACCCTTGGTTTGT
* * *
41966565 AAAATTACTAAAATACCATTGGTTTAT
1 AAAATTACCAAAATACCCTTGGTTTGT
* *
41966592 AAAATCACCAAAATACCCTTTGTTTGT
1 AAAATTACCAAAATACCCTTGGTTTGT
**
41966619 AAAATTACCAAAATACCCTTGGTTTAC
1 AAAATTACCAAAATACCCTTGGTTTGT
41966646 AAAATTACCAAAATACCCTTGGTTTGT
1 AAAATTACCAAAATACCCTTGGTTTGT
* * *
41966673 AAAATTACTAAAATACCATTGGTTTAT
1 AAAATTACCAAAATACCCTTGGTTTGT
* *
41966700 AAAATCACCAAAATACCCTTTGTTTGT
1 AAAATTACCAAAATACCCTTGGTTTGT
**
41966727 AAAATTACCAAAATACCCTTGGTTTAC
1 AAAATTACCAAAATACCCTTGGTTTGT
41966754 AAAATTACCAAAATACCCTTGGTTTGT
1 AAAATTACCAAAATACCCTTGGTTTGT
* * *
41966781 AAAATTACTAAAATACCATTGGTTTAT
1 AAAATTACCAAAATACCCTTGGTTTGT
* *
41966808 AAAATCACCAAAATACCCTTTGTTTGT
1 AAAATTACCAAAATACCCTTGGTTTGT
**
41966835 AAAATTACCAAAATACCCTTGGTTTAC
1 AAAATTACCAAAATACCCTTGGTTTGT
41966862 AAAATTACCAAAATACCCTTGGTTTGT
1 AAAATTACCAAAATACCCTTGGTTTGT
* * *
41966889 AAAATTACTAAAATACCATTGGTTTAT
1 AAAATTACCAAAATACCCTTGGTTTGT
* *
41966916 AAAATCACCAAAATACCCTTTGTTTGT
1 AAAATTACCAAAATACCCTTGGTTTGT
**
41966943 AAAATTACCAAAATACCCTTGGTTTAC
1 AAAATTACCAAAATACCCTTGGTTTGT
*
41966970 AAAATTACCAAAATACCCTTAGTTTGT
1 AAAATTACCAAAATACCCTTGGTTTGT
* * *
41966997 AAAATTACTAAAATACCATTGGTTTAT
1 AAAATTACCAAAATACCCTTGGTTTGT
* *
41967024 AAAATTACCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCTTGGTTTGT
* *
41967051 AAAATTACCAAAATACCCCTGATTTGT
1 AAAATTACCAAAATACCCTTGGTTTGT
* ** * **
41967078 GAAATTACTGAAATACCCTCGACTTGT
1 AAAATTACCAAAATACCCTTGGTTTGT
*** * **
41967105 AAAATTATTGAAATACCCTCGACTTGT
1 AAAATTACCAAAATACCCTTGGTTTGT
*
41967132 AAAATTA-CAAAGTACC
1 AAAATTACCAAAATACC
41967148 ATTGATTTAC
Statistics
Matches: 924, Mismatches: 141, Indels: 33
0.84 0.13 0.03
Matches are distributed among these distances:
26 12 0.01
27 879 0.95
28 8 0.01
30 2 0.00
32 1 0.00
33 2 0.00
34 1 0.00
36 2 0.00
38 3 0.00
39 14 0.02
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.32
Consensus pattern (27 bp):
AAAATTACCAAAATACCCTTGGTTTGT
Found at i:41967109 original size:108 final size:108
Alignment explanation
Indices: 41966040--41967068 Score: 1639
Period size: 108 Copynumber: 9.4 Consensus size: 108
41966030 TTTAGTTCAC
* * * * * *
41966040 AAAATTACCAAAATACCC-CTGATTTGTAAAATTACTAAAATACCCTTGGTTTATAAAATCATCA
1 AAAATCACCAAAATACCCTTTG-TTTGTAAAATTACCAAAATACCCTTGGTTTACAAAATTACCA
* *
41966104 AAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTGGTTTAT
65 AAATACCCTTGGTTTGTAAAATTACTAAAATACCATTGGTTTAT
* * * *
41966148 AAAATCACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCATTAGTTTACAAAATTACCAA
1 AAAATCACCAAAATACCCTTTGTTTGTAAAATTACCAAAATACCCTTGGTTTACAAAATTACCAA
41966213 AATACCCTTGGTTTGTAAAATTACTAAAATACCATTGGTTTAT
66 AATACCCTTGGTTTGTAAAATTACTAAAATACCATTGGTTTAT
*
41966256 AAAATCACCAAAATACCCTTAGTTTGTAAAATTACCAAAATACCCTTGGTTTACAAAATTACCAA
1 AAAATCACCAAAATACCCTTTGTTTGTAAAATTACCAAAATACCCTTGGTTTACAAAATTACCAA
* * ** * *
41966321 AATACCCTTAGTTTGTAAAATTACCAAAATACCCCTAGTTTGT
66 AATACCCTTGGTTTGTAAAATTACTAAAATACCATTGGTTTAT
* * * * **
41966364 AAAATTACCAAAATACCAC-TGGTTTGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCA
1 AAAATCACCAAAATACC-CTTTGTTTGTAAAATTACCAAAATACCCTTGGTTTACAAAATTACCA
41966428 AAATACCCCTGATTTGTGAATTAGTTTGTAAAATTACTAAAATACCATTGGTTTAT
65 AAATA-CCC-----T-TG-----GTTTGTAAAATTACTAAAATACCATTGGTTTAT
* *
41966484 AAAATTACCAAAATACCCCTTGTTTGTAAAATTACCAAAATACCCTTGGTTTACAAAATTACCAA
1 AAAATCACCAAAATACCCTTTGTTTGTAAAATTACCAAAATACCCTTGGTTTACAAAATTACCAA
41966549 AATACCCTTGGTTTGTAAAATTACTAAAATACCATTGGTTTAT
66 AATACCCTTGGTTTGTAAAATTACTAAAATACCATTGGTTTAT
41966592 AAAATCACCAAAATACCCTTTGTTTGTAAAATTACCAAAATACCCTTGGTTTACAAAATTACCAA
1 AAAATCACCAAAATACCCTTTGTTTGTAAAATTACCAAAATACCCTTGGTTTACAAAATTACCAA
41966657 AATACCCTTGGTTTGTAAAATTACTAAAATACCATTGGTTTAT
66 AATACCCTTGGTTTGTAAAATTACTAAAATACCATTGGTTTAT
41966700 AAAATCACCAAAATACCCTTTGTTTGTAAAATTACCAAAATACCCTTGGTTTACAAAATTACCAA
1 AAAATCACCAAAATACCCTTTGTTTGTAAAATTACCAAAATACCCTTGGTTTACAAAATTACCAA
41966765 AATACCCTTGGTTTGTAAAATTACTAAAATACCATTGGTTTAT
66 AATACCCTTGGTTTGTAAAATTACTAAAATACCATTGGTTTAT
41966808 AAAATCACCAAAATACCCTTTGTTTGTAAAATTACCAAAATACCCTTGGTTTACAAAATTACCAA
1 AAAATCACCAAAATACCCTTTGTTTGTAAAATTACCAAAATACCCTTGGTTTACAAAATTACCAA
41966873 AATACCCTTGGTTTGTAAAATTACTAAAATACCATTGGTTTAT
66 AATACCCTTGGTTTGTAAAATTACTAAAATACCATTGGTTTAT
41966916 AAAATCACCAAAATACCCTTTGTTTGTAAAATTACCAAAATACCCTTGGTTTACAAAATTACCAA
1 AAAATCACCAAAATACCCTTTGTTTGTAAAATTACCAAAATACCCTTGGTTTACAAAATTACCAA
*
41966981 AATACCCTTAGTTTGTAAAATTACTAAAATACCATTGGTTTAT
66 AATACCCTTGGTTTGTAAAATTACTAAAATACCATTGGTTTAT
* * *
41967024 AAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCC
1 AAAATCACCAAAATACCCTTTGTTTGTAAAATTACCAAAATACCC
41967069 CTGATTTGTG
Statistics
Matches: 862, Mismatches: 44, Indels: 30
0.92 0.05 0.03
Matches are distributed among these distances:
108 758 0.88
109 5 0.01
113 2 0.00
114 2 0.00
115 1 0.00
119 4 0.00
120 90 0.10
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.32
Consensus pattern (108 bp):
AAAATCACCAAAATACCCTTTGTTTGTAAAATTACCAAAATACCCTTGGTTTACAAAATTACCAA
AATACCCTTGGTTTGTAAAATTACTAAAATACCATTGGTTTAT
Found at i:41967255 original size:80 final size:79
Alignment explanation
Indices: 41967182--41967402 Score: 199
Period size: 80 Copynumber: 2.7 Consensus size: 79
41967172 ACCCTCAATT
** * * *
41967182 TACAAATTACCGAAATACCCTTGTAGGGTAGAAATGCCGAAATACCCTTGTAGGGTAGAAATACC
1 TACAAA-TACCGAAATACCC-CATAGGGTAGAAATACCAAAATACCCCTGTAGGGTAGAAATACC
* *
41967247 GAAATACCCCTGTAGGG
64 GAAATA-CCCTGCAAGG
* * * * *
41967264 TAGAAATACCGAAATACCCCATAGGGTAGAATTACTAAAATACCCCTGTAGGGTAGAATTATCGA
1 TACAAATACCGAAATACCCCATAGGGTAGAAATACCAAAATACCCCTGTAGGGTAGAAATACCGA
* *
41967329 AATACCCTTGTAGGG
66 AATACCC-TGCAAGG
* ** * ** * *
41967344 TAGAAATACCGAAATACTCCTGTAGGGTAGAATTACTGAAATACTCCTGTAAGGTAGAA
1 TACAAATACCGAAATAC-CCCATAGGGTAGAAATACCAAAATACCCCTGTAGGGTAGAA
41967403 TTACTAAGAT
Statistics
Matches: 122, Mismatches: 15, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
79 3 0.02
80 65 0.53
81 49 0.40
82 5 0.04
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.24
Consensus pattern (79 bp):
TACAAATACCGAAATACCCCATAGGGTAGAAATACCAAAATACCCCTGTAGGGTAGAAATACCGA
AATACCCTGCAAGG
Found at i:41967305 original size:107 final size:108
Alignment explanation
Indices: 41967194--41967418 Score: 344
Period size: 107 Copynumber: 2.1 Consensus size: 108
41967184 CAAATTACCG
*
41967194 AAATACCCTTGTAGGGTAGAAATGCCGAAATACCCTTGTAGGGTAGAAATACCGAAATACCCCTG
1 AAATACCCTTGTAGGGTAGAAATACCGAAATACCCTTGTAGGGTAGAAATACCGAAATACCCCTG
*
41967259 TAGGGTAGAAATACCGAAATAC-CCCATAGGGTAGAATTACTA
66 TAGGGTAGAAATACCGAAATACTCCCATAAGGTAGAATTACTA
* * * *
41967301 AAATACCCCTGTAGGGTAGAATTATCGAAATACCCTTGTAGGGTAGAAATACCGAAATACTCCTG
1 AAATACCCTTGTAGGGTAGAAATACCGAAATACCCTTGTAGGGTAGAAATACCGAAATACCCCTG
* * **
41967366 TAGGGTAGAATTACTGAAATACTCCTGTAAGGTAGAATTACTA
66 TAGGGTAGAAATACCGAAATACTCCCATAAGGTAGAATTACTA
*
41967409 AGATACCCTT
1 AAATACCCTT
41967419 ATGGGGTAAA
Statistics
Matches: 105, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
107 80 0.76
108 25 0.24
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.24
Consensus pattern (108 bp):
AAATACCCTTGTAGGGTAGAAATACCGAAATACCCTTGTAGGGTAGAAATACCGAAATACCCCTG
TAGGGTAGAAATACCGAAATACTCCCATAAGGTAGAATTACTA
Found at i:41967407 original size:27 final size:26
Alignment explanation
Indices: 41967186--41967406 Score: 271
Period size: 27 Copynumber: 8.2 Consensus size: 26
41967176 TCAATTTACA
41967186 AATTACCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCC-TGTAGGGTAG
* *
41967213 AAATGCCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCC-TGTAGGGTAG
*
41967240 AAATACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATA-CCCTGTAGGGTAG
* **
41967267 AAATACCGAAATACCCCATAGGGTAG
1 AATTACCGAAATACCCTGTAGGGTAG
**
41967293 AATTACTAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATA-CCCTGTAGGGTAG
*
41967320 AATTATCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCC-TGTAGGGTAG
*
41967347 AAATACCGAAATACTCCTGTAGGGTAG
1 AATTACCGAAATAC-CCTGTAGGGTAG
* *
41967374 AATTACTGAAATACTCCTGTAAGGTAG
1 AATTACCGAAATAC-CCTGTAGGGTAG
41967401 AATTAC
1 AATTAC
41967407 TAAGATACCC
Statistics
Matches: 172, Mismatches: 18, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
26 24 0.14
27 143 0.83
28 5 0.03
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.24
Consensus pattern (26 bp):
AATTACCGAAATACCCTGTAGGGTAG
Found at i:41967426 original size:27 final size:25
Alignment explanation
Indices: 41967194--41967433 Score: 112
Period size: 27 Copynumber: 9.0 Consensus size: 25
41967184 CAAATTACCG
* ** *
41967194 AAATACCCTTGTAGGGTAGAAATGCCG
1 AAATACCCTTAT-GGGTAG-AATTACT
* * *
41967221 AAATACCCTTGTAGGGTAGAAATACCG
1 AAATACCCTTAT-GGGTAGAATTA-CT
* *
41967248 AAATACCCCTGTA-GGGTAGAAATACCG
1 AAATA-CCCT-TATGGGTAGAATTA-CT
*
41967275 AAATACCC-CATAGGGTAGAATTACT
1 AAATACCCTTAT-GGGTAGAATTACT
*
41967300 AAAATACCCCTGTA-GGGTAGAATTATCG
1 -AAATA-CCCT-TATGGGTAGAATTA-CT
* * *
41967328 AAATACCCTTGTAGGGTAGAAATACCG
1 AAATACCCTTAT-GGGTAGAATTA-CT
41967355 AAATACTCCTGTA-GGGTAGAATTACT
1 AAATAC-CCT-TATGGGTAGAATTACT
*
41967381 GAAATACTCCTGTA-AGGTAGAATTACT
1 -AAATAC-CCT-TATGGGTAGAATTACT
*
41967408 AAGATACCCTTATGGGGTAAAATTAC
1 AA-ATACCCTTAT-GGGTAGAATTAC
41967434 CATTTTACCC
Statistics
Matches: 177, Mismatches: 18, Indels: 36
0.77 0.08 0.16
Matches are distributed among these distances:
24 1 0.01
25 4 0.02
26 30 0.17
27 131 0.74
28 8 0.05
29 3 0.02
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.25
Consensus pattern (25 bp):
AAATACCCTTATGGGTAGAATTACT
Found at i:41967426 original size:54 final size:51
Alignment explanation
Indices: 41967194--41967433 Score: 182
Period size: 54 Copynumber: 4.5 Consensus size: 51
41967184 CAAATTACCG
* * * * * *
41967194 AAATACCCTTGTAGGGTAGAAATGCCGAAATACCCTTGTAGGGTAGAAATACCG
1 AAATACCCTTAT-GGGTAGAATTACTGAAATACCC-TGTAGGGTAGAATTA-CT
* * **
41967248 AAATACCCCTGTA-GGGTAGAAATACCGAAATACCCCATAGGGTAGAATTACT
1 AAATA-CCCT-TATGGGTAGAATTACTGAAATACCCTGTAGGGTAGAATTACT
* *
41967300 AAAATACCCCTGTA-GGGTAGAATTA-TCGAAATACCCTTGTAGGGTAGAAATACCG
1 -AAATA-CCCT-TATGGGTAGAATTACT-GAAATACCC-TGTAGGGTAGAATTA-CT
*
41967355 AAATACTCCTGTA-GGGTAGAATTACTGAAATACTCCTGTAAGGTAGAATTACT
1 AAATAC-CCT-TATGGGTAGAATTACTGAAATAC-CCTGTAGGGTAGAATTACT
*
41967408 AAGATACCCTTATGGGGTAAAATTAC
1 AA-ATACCCTTAT-GGGTAGAATTAC
41967434 CATTTTACCC
Statistics
Matches: 158, Mismatches: 16, Indels: 24
0.80 0.08 0.12
Matches are distributed among these distances:
52 3 0.02
53 51 0.32
54 95 0.60
55 8 0.05
56 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.25
Consensus pattern (51 bp):
AAATACCCTTATGGGTAGAATTACTGAAATACCCTGTAGGGTAGAATTACT
Found at i:41967857 original size:6 final size:6
Alignment explanation
Indices: 41967848--41967963 Score: 76
Period size: 6 Copynumber: 18.8 Consensus size: 6
41967838 TTGCATTCAC
* *
41967848 ATTCTG ATTCTG ATTCTG -TTACCTG ATACTG ATTCTG ATTCTG -TTACCTA
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATT--CTG
* * * * *
41967898 ATTCTA ATTCTG ATTCTG ATTTTG ATTTTG -TTACCTG ATTTTG ATTCTC
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG
* *
41967947 ATTTTG ATTCTA ATTCT
1 ATTCTG ATTCTG ATTCT
41967964 AATAATGTTT
Statistics
Matches: 88, Mismatches: 13, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
5 6 0.07
6 70 0.80
7 7 0.08
8 5 0.06
ACGTcount: A:0.20, C:0.16, G:0.12, T:0.52
Consensus pattern (6 bp):
ATTCTG
Found at i:41967879 original size:25 final size:25
Alignment explanation
Indices: 41967851--41967915 Score: 103
Period size: 25 Copynumber: 2.6 Consensus size: 25
41967841 CATTCACATT
*
41967851 CTGATTCTGATTCTGTTACCTGATA
1 CTGATTCTGATTCTGTTACCTAATA
*
41967876 CTGATTCTGATTCTGTTACCTAATT
1 CTGATTCTGATTCTGTTACCTAATA
*
41967901 CTAATTCTGATTCTG
1 CTGATTCTGATTCTG
41967916 ATTTTGATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.46
Consensus pattern (25 bp):
CTGATTCTGATTCTGTTACCTAATA
Found at i:41967883 original size:31 final size:31
Alignment explanation
Indices: 41967848--41967957 Score: 100
Period size: 31 Copynumber: 3.5 Consensus size: 31
41967838 TTGCATTCAC
*
41967848 ATTCTGATTCTGATTCTGTTACCTGATACTG
1 ATTCTGATTCTGATTCTGTTACCTGATTCTG
* *
41967879 ATTCTGATTCTG-TTACCTAATT--CTAATTCTG
1 ATTCTGATTCTGATT--CT-GTTACCTGATTCTG
* * *
41967910 ATTCTGATTTTGATTTTGTTACCTGATTTTG
1 ATTCTGATTCTGATTCTGTTACCTGATTCTG
* *
41967941 ATTCTCATTTTGATTCT
1 ATTCTGATTCTGATTCT
41967958 AATTCTAATA
Statistics
Matches: 63, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
29 2 0.03
30 3 0.05
31 52 0.83
32 4 0.06
33 2 0.03
ACGTcount: A:0.19, C:0.16, G:0.13, T:0.52
Consensus pattern (31 bp):
ATTCTGATTCTGATTCTGTTACCTGATTCTG
Found at i:41967901 original size:19 final size:19
Alignment explanation
Indices: 41967876--41967945 Score: 72
Period size: 19 Copynumber: 3.7 Consensus size: 19
41967866 TTACCTGATA
41967876 CTGATTCTGATTCTGTTAC
1 CTGATTCTGATTCTGTTAC
* *
41967895 CTAATTCTAATTCTGATT--
1 CTGATTCTGATTCTG-TTAC
* *
41967913 CTGATTTTGATTTTGTTAC
1 CTGATTCTGATTCTGTTAC
*
41967932 CTGATTTTGATTCT
1 CTGATTCTGATTCT
41967946 CATTTTGATT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
17 2 0.05
18 11 0.27
19 26 0.63
20 2 0.05
ACGTcount: A:0.19, C:0.16, G:0.13, T:0.53
Consensus pattern (19 bp):
CTGATTCTGATTCTGTTAC
Found at i:41967945 original size:37 final size:37
Alignment explanation
Indices: 41967870--41967963 Score: 107
Period size: 37 Copynumber: 2.5 Consensus size: 37
41967860 ATTCTGTTAC
*
41967870 CTGATACTGATTCTGATTCTGTTACCTAATTCTAATT
1 CTGATTCTGATTCTGATTCTGTTACCTAATTCTAATT
* * * * *
41967907 CTGATTCTGATTTTGATTTTGTTACCTGATTTTGATT
1 CTGATTCTGATTCTGATTCTGTTACCTAATTCTAATT
* * *
41967944 CTCATTTTGATTCTAATTCT
1 CTGATTCTGATTCTGATTCT
41967964 AATAATGTTT
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.20, C:0.16, G:0.12, T:0.52
Consensus pattern (37 bp):
CTGATTCTGATTCTGATTCTGTTACCTAATTCTAATT
Found at i:41970065 original size:54 final size:54
Alignment explanation
Indices: 41969937--41970391 Score: 466
Period size: 54 Copynumber: 8.4 Consensus size: 54
41969927 GAATACTTTA
* * * * **
41969937 GTTTACCAAATTACCAAAATACCACTGGTTTGTAAAATTACTAAAAT-CTTTTG
1 GTTTACAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTG
* * * *
41969990 GTTTATAAAATCACCAAAATACCCTTTGTTTGTAAAATTACCAAAATACCCTTG
1 GTTTACAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTG
* *
41970044 GTTTACAAAATTACCAAAATACCCCTAGTTTATAAAATTATCAAAATACCCTTG
1 GTTTACAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTG
* *
41970098 GTTTACAAAATTACCAAAATACCCCTAGTTTATAAAATTATCAAAATACCCTTG
1 GTTTACAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTG
* ** *
41970152 GTTTACAAAATTACCAAAATACCCCTGGTTTGTAAAATTAGTAAAATACCATTG
1 GTTTACAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTG
* *
41970206 GTTTATAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTG
1 GTTTACAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTG
* * ** * ** *** *
41970260 ATTT-CTGAAATTACTGAAATA-CCCTCGACCTGTAAAATTATTGAAATACCCTCG
1 GTTTAC-AAAATTACCAAAATACCCCTAG-TTTGTAAAATTACCAAAATACCCTTG
** ** * *** * * *
41970314 ACTTGTAAAATTACCAAAGTACTATTGAGTTTGTAAAATTATCAAAATACCCCTA
1 GTTTACAAAATTACCAAAATACCCCT-AGTTTGTAAAATTACCAAAATACCCTTG
**
41970369 GTTTGTAAAATTACCAAAATACC
1 GTTTACAAAATTACCAAAATACC
41970392 TTTGATTTCT
Statistics
Matches: 336, Mismatches: 60, Indels: 10
0.83 0.15 0.02
Matches are distributed among these distances:
53 45 0.13
54 251 0.75
55 39 0.12
56 1 0.00
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.32
Consensus pattern (54 bp):
GTTTACAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTG
Found at i:41970398 original size:136 final size:136
Alignment explanation
Indices: 41970070--41970491 Score: 530
Period size: 136 Copynumber: 3.1 Consensus size: 136
41970060 AAATACCCCT
* * * ** * *
41970070 AGTTTATAAAATTATCAAAATACCCTTGGTTTACAAAATTACCAAAATACCCCT-AGTTTATAAA
1 AGTTTATAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGA-TTTCTGAA
* * *** ** *** ** **
41970134 ATTA-TCAAAATACCCTTGGTTTACAAAATTACCAAAATACCC-CTGGTTTGTAAAATTAGTAAA
65 ATTACT-GAAATACCCTCGACCTGTAAAATTATTGAAATACCCTC-GACTTGTAAAATTACCAAA
* *
41970197 ATACCATTG
128 GTACTATTG
41970206 -GTTTATAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGATTTCTGAAA
1 AGTTTATAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGATTTCTGAAA
41970270 TTACTGAAATACCCTCGACCTGTAAAATTATTGAAATACCCTCGACTTGTAAAATTACCAAAGTA
66 TTACTGAAATACCCTCGACCTGTAAAATTATTGAAATACCCTCGACTTGTAAAATTACCAAAGTA
41970335 CTATTG
131 CTATTG
* * **
41970341 AGTTTGTAAAATTATCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCTTTGATTTCTGAAA
1 AGTTTATAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGATTTCTGAAA
41970406 TTACTGAAATACCCTCGACCTGTAAAATTATTGAAATACCCTCGACTTGTAAAATTACCAAAGTA
66 TTACTGAAATACCCTCGACCTGTAAAATTATTGAAATACCCTCGACTTGTAAAATTACCAAAGTA
41970471 CTATTG
131 CTATTG
*
41970477 A-TTTATAGAATTACC
1 AGTTTATAAAATTACC
41970492 GTTTTACCCT
Statistics
Matches: 252, Mismatches: 30, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
135 117 0.46
136 135 0.54
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.32
Consensus pattern (136 bp):
AGTTTATAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGATTTCTGAAA
TTACTGAAATACCCTCGACCTGTAAAATTATTGAAATACCCTCGACTTGTAAAATTACCAAAGTA
CTATTG
Found at i:41970406 original size:27 final size:27
Alignment explanation
Indices: 41969944--41970491 Score: 390
Period size: 27 Copynumber: 20.3 Consensus size: 27
41969934 TTAGTTTACC
*
41969944 AAATTACCAAAATACCAC-TGGTTTGTA
1 AAATTACCAAAATACC-CTTGATTTGTA
* ** * *
41969971 AAATTACTAAAAT-CTTTTGGTTTATA
1 AAATTACCAAAATACCCTTGATTTGTA
*
41969997 AAATCACCAAAATACCCTTTG-TTTGTA
1 AAATTACCAAAATACCC-TTGATTTGTA
* **
41970024 AAATTACCAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCTTGATTTGTA
* *
41970051 AAATTACCAAAATACCCCT-AGTTTATA
1 AAATTACCAAAATACCCTTGA-TTTGTA
* * **
41970078 AAATTATCAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCTTGATTTGTA
* *
41970105 AAATTACCAAAATACCCCT-AGTTTATA
1 AAATTACCAAAATACCCTTGA-TTTGTA
* * **
41970132 AAATTATCAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCTTGATTTGTA
* *
41970159 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCTTGATTTGTA
** * * *
41970186 AAATTAGTAAAATACCATTGGTTTATA
1 AAATTACCAAAATACCCTTGATTTGTA
*
41970213 AAATTACCAAAATACCCCT-AGTTTGTA
1 AAATTACCAAAATACCCTTGA-TTTGTA
* * *
41970240 AAATTACCAAAATACCCCTGATTTCTG
1 AAATTACCAAAATACCCTTGATTTGTA
** * **
41970267 AAATTACTGAAATACCCTCGACCTGTA
1 AAATTACCAAAATACCCTTGATTTGTA
*** * *
41970294 AAATTATTGAAATACCCTCGACTTGTA
1 AAATTACCAAAATACCCTTGATTTGTA
* **
41970321 AAATTACCAAAGTACTATTGAGTTTGTA
1 AAATTACCAAAATACCCTTGA-TTTGTA
* *
41970349 AAATTATCAAAATACCCCT-AGTTTGTA
1 AAATTACCAAAATACCCTTGA-TTTGTA
* * *
41970376 AAATTACCAAAATACCTTTGATTTCTG
1 AAATTACCAAAATACCCTTGATTTGTA
** * **
41970403 AAATTACTGAAATACCCTCGACCTGTA
1 AAATTACCAAAATACCCTTGATTTGTA
*** * *
41970430 AAATTATTGAAATACCCTCGACTTGTA
1 AAATTACCAAAATACCCTTGATTTGTA
* ** *
41970457 AAATTACCAAAGTACTATTGATTTATA
1 AAATTACCAAAATACCCTTGATTTGTA
*
41970484 GAATTACC
1 AAATTACC
41970492 GTTTTACCCT
Statistics
Matches: 417, Mismatches: 92, Indels: 24
0.78 0.17 0.05
Matches are distributed among these distances:
26 23 0.06
27 370 0.89
28 24 0.06
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.32
Consensus pattern (27 bp):
AAATTACCAAAATACCCTTGATTTGTA
Found at i:41970430 original size:54 final size:54
Alignment explanation
Indices: 41970292--41970435 Score: 159
Period size: 55 Copynumber: 2.6 Consensus size: 54
41970282 CCTCGACCTG
* *
41970292 TAAAATTATTGAAATACCCTCGACTTGTAAAATTACCAAAGTACTATTGAGTTTG
1 TAAAATTA-TGAAATACCCTCGACTTGTAAAATTACCAAAATACTATTGAGTTTC
* * *
41970347 TAAAATTATCAAAATACCC-CTAGTTTGTAAAATTACCAAAATACCT-TTGA-TTTC
1 TAAAATTAT-GAAATACCCTCGA-CTTGTAAAATTACCAAAATA-CTATTGAGTTTC
* *
41970401 TGAAATTACTGAAATACCCTCGACCTGTAAAATTA
1 TAAAATTA-TGAAATACCCTCGACTTGTAAAATTA
41970436 TTGAAATACC
Statistics
Matches: 74, Mismatches: 10, Indels: 11
0.78 0.11 0.12
Matches are distributed among these distances:
54 31 0.42
55 41 0.55
56 2 0.03
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (54 bp):
TAAAATTATGAAATACCCTCGACTTGTAAAATTACCAAAATACTATTGAGTTTC
Found at i:41970500 original size:81 final size:82
Alignment explanation
Indices: 41970345--41970528 Score: 196
Period size: 81 Copynumber: 2.3 Consensus size: 82
41970335 CTATTGAGTT
* * * *
41970345 TGTAAAATTATCAAAATACCC-CTAGTTTGTAAAATTACCAAAATACCTTTGATTTCTGAAATTA
1 TGTAAAATTATCGAAATACCCTCGAGCTTGTAAAATTACCAAAATACCTTTGATTTATGAAATTA
*
41970409 CTGAAATACCCTCGACC
66 CCGAAATACCCTCGACC
* *
41970426 TGTAAAATTATTGAAATACCCTCGA-CTTGTAAAATTACCAAAGTA-CTATTGATTTAT-AGAAT
1 TGTAAAATTATCGAAATACCCTCGAGCTTGTAAAATTACCAAAATACCT-TTGATTTATGA-AAT
*** **
41970488 TACCGTTTTACCCTCGATT
64 TACCGAAATACCCTCGACC
**
41970507 TACAAAATTATCGAAATACCCT
1 TGTAAAATTATCGAAATACCCT
41970529 TGTAGGGTAG
Statistics
Matches: 85, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
80 3 0.04
81 80 0.94
82 2 0.02
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.34
Consensus pattern (82 bp):
TGTAAAATTATCGAAATACCCTCGAGCTTGTAAAATTACCAAAATACCTTTGATTTATGAAATTA
CCGAAATACCCTCGACC
Found at i:41970542 original size:136 final size:136
Alignment explanation
Indices: 41970181--41970530 Score: 427
Period size: 136 Copynumber: 2.6 Consensus size: 136
41970171 TACCCCTGGT
** * * * **
41970181 TTGTAAAATTAGTAAAATACCATTG-GTTTATAAAATTACCAAAATACCCCTAGTTTGTAAAATT
1 TTGTAAAATTACCAAAGTACTATTGAGTTTATAAAATTACCAAAATACCCCGAGTTTACAAAATT
* ** *
41970245 ACCAAAATACCCCTGATTTCTGAAATTACTGAAATACCCTCGACCTGTAAAATTATTGAAATACC
66 ACCAAAATACCCTTGAGGTCAGAAATTACTGAAATACCCTCGACCTGTAAAATTATTGAAATACC
41970310 CTCGAC
131 CTCGAC
* * * **
41970316 TTGTAAAATTACCAAAGTACTATTGAGTTTGTAAAATTATCAAAATACCCCTAGTTTGTAAAATT
1 TTGTAAAATTACCAAAGTACTATTGAGTTTATAAAATTACCAAAATACCCCGAGTTTACAAAATT
* ** *
41970381 ACCAAAATACCTTTGATTTCTGAAATTACTGAAATACCCTCGACCTGTAAAATTATTGAAATACC
66 ACCAAAATACCCTTGAGGTCAGAAATTACTGAAATACCCTCGACCTGTAAAATTATTGAAATACC
41970446 CTCGAC
131 CTCGAC
* ****
41970452 TTGTAAAATTACCAAAGTACTATTGA-TTTATAGAATTACCGTTTTACCCTCGA-TTTACAAAAT
1 TTGTAAAATTACCAAAGTACTATTGAGTTTATAAAATTACCAAAATACCC-CGAGTTTACAAAAT
* *
41970515 TATCGAAATACCCTTG
65 TACCAAAATACCCTTG
41970531 TAGGGTAGAA
Statistics
Matches: 192, Mismatches: 21, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
135 58 0.30
136 134 0.70
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (136 bp):
TTGTAAAATTACCAAAGTACTATTGAGTTTATAAAATTACCAAAATACCCCGAGTTTACAAAATT
ACCAAAATACCCTTGAGGTCAGAAATTACTGAAATACCCTCGACCTGTAAAATTATTGAAATACC
CTCGAC
Found at i:41970550 original size:27 final size:27
Alignment explanation
Indices: 41970520--41970761 Score: 249
Period size: 27 Copynumber: 9.0 Consensus size: 27
41970510 AAAATTATCG
*
41970520 AAATACCCTTGTAGGGTAGAAATGCCA
1 AAATACCCTTGTAGGGTAGAAATACCA
*
41970547 AAATACCCTTGTAGGGTAGAAATACCG
1 AAATACCCTTGTAGGGTAGAAATACCA
* *
41970574 AAATACCCCTGTAGGGTAGAAATACTA
1 AAATACCCTTGTAGGGTAGAAATACCA
* *
41970601 AAATACCCCTGTAGGGTA-AAATTACTA
1 AAATACCCTTGTAGGGTAGAAA-TACCA
* *
41970628 AAATACCCTTGTAGGGTAGAATTACCG
1 AAATACCCTTGTAGGGTAGAAATACCA
* * *
41970655 AAATACCCTTGTA-GGTAGAATTATCG
1 AAATACCCTTGTAGGGTAGAAATACCA
* * *
41970681 AAATACCCCTGTAGGGTAGAATTACTA
1 AAATACCCTTGTAGGGTAGAAATACCA
* * * *
41970708 AAATATTCC-TGTAAGGTAGAATTACCG
1 AAATA-CCCTTGTAGGGTAGAAATACCA
* *
41970735 AGATACCCTTGTGGGGTA-AAATTACCA
1 AAATACCCTTGTAGGGTAGAAA-TACCA
41970762 TTTTACCCCT
Statistics
Matches: 185, Mismatches: 24, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
26 31 0.17
27 150 0.81
28 4 0.02
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.26
Consensus pattern (27 bp):
AAATACCCTTGTAGGGTAGAAATACCA
Found at i:41970719 original size:107 final size:108
Alignment explanation
Indices: 41970510--41970761 Score: 344
Period size: 107 Copynumber: 2.3 Consensus size: 108
41970500 CTCGATTTAC
* * * *
41970510 AAAATTATCGAAATACCCTTGTAGGGTAGAAATGCCAAAATACCCTTGTAGGGTAGAAATACCGA
1 AAAATTACCAAAATACCCTTGTAGGGTAGAATTACCAAAATACCCTTGTAGGGTAGAAATACCGA
*
41970575 AATACCCCTGTAGGGTAGAAATACTAAAATACCCCTGTAGGGT
66 AATACCCCTGTAGGGTAGAAATACTAAAATACCCCTGTAAGGT
* * * *
41970618 AAAATTACTAAAATACCCTTGTAGGGTAGAATTACCGAAATACCCTTGTA-GGTAGAATTATCGA
1 AAAATTACCAAAATACCCTTGTAGGGTAGAATTACCAAAATACCCTTGTAGGGTAGAAATACCGA
* **
41970682 AATACCCCTGTAGGGTAGAATTACTAAAATATTCCTGTAAGGT
66 AATACCCCTGTAGGGTAGAAATACTAAAATACCCCTGTAAGGT
* * * * *
41970725 AGAATTACCGAGATACCCTTGTGGGGTAAAATTACCA
1 AAAATTACCAAAATACCCTTGTAGGGTAGAATTACCA
41970762 TTTTACCCCT
Statistics
Matches: 125, Mismatches: 19, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
107 81 0.65
108 44 0.35
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.26
Consensus pattern (108 bp):
AAAATTACCAAAATACCCTTGTAGGGTAGAATTACCAAAATACCCTTGTAGGGTAGAAATACCGA
AATACCCCTGTAGGGTAGAAATACTAAAATACCCCTGTAAGGT
Found at i:41970726 original size:80 final size:81
Alignment explanation
Indices: 41970512--41970758 Score: 329
Period size: 81 Copynumber: 3.1 Consensus size: 81
41970502 CGATTTACAA
* * * * *
41970512 AATTATCGAAATACCCTTGTAGGGTAGAAATGCCAAAATACCCTTGTAGGGTAGAAATACCGAAA
1 AATTATCGAAATACCCCTGTAGGGTAGAATTACTAAAATACCCTTGTAGGGTAGAATTACCGAAA
*
41970577 TACCCCTGTAGGGTAG
66 TACCCTTGTAGGGTAG
* * *
41970593 AAATA-CTAAAATACCCCTGTAGGGTAAAATTACTAAAATACCCTTGTAGGGTAGAATTACCGAA
1 AATTATC-GAAATACCCCTGTAGGGTAGAATTACTAAAATACCCTTGTAGGGTAGAATTACCGAA
41970657 ATACCCTTGTA-GGTAG
65 ATACCCTTGTAGGGTAG
* * *
41970673 AATTATCGAAATACCCCTGTAGGGTAGAATTACTAAAATATTCC-TGTAAGGTAGAATTACCGAG
1 AATTATCGAAATACCCCTGTAGGGTAGAATTACTAAAATA-CCCTTGTAGGGTAGAATTACCGAA
* *
41970737 ATACCCTTGTGGGGTAA
65 ATACCCTTGTAGGGTAG
41970754 AATTA
1 AATTA
41970759 CCATTTTACC
Statistics
Matches: 145, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
80 69 0.48
81 76 0.52
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (81 bp):
AATTATCGAAATACCCCTGTAGGGTAGAATTACTAAAATACCCTTGTAGGGTAGAATTACCGAAA
TACCCTTGTAGGGTAG
Found at i:41970752 original size:54 final size:54
Alignment explanation
Indices: 41970512--41970761 Score: 288
Period size: 54 Copynumber: 4.6 Consensus size: 54
41970502 CGATTTACAA
* * * *
41970512 AATTATCGAAATACCCTTGTAGGGTAGAAATGCCAAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAGAATTACCAAAATACCCTTGTAAGGTAG
* * * * * * *
41970566 AAATACCGAAATACCCCTGTAGGGTAGAAATACTAAAATACCCCTGTAGGGTAA
1 AATTACCGAAATACCCTTGTAGGGTAGAATTACCAAAATACCCTTGTAAGGTAG
** *
41970620 AATTACTAAAATACCCTTGTAGGGTAGAATTACCGAAATACCCTTGT-AGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAGAATTACCAAAATACCCTTGTAAGGTAG
* * * *
41970673 AATTATCGAAATACCCCTGTAGGGTAGAATTACTAAAATATTCC-TGTAAGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAGAATTACCAAAATA-CCCTTGTAAGGTAG
* * *
41970727 AATTACCGAGATACCCTTGTGGGGTAAAATTACCA
1 AATTACCGAAATACCCTTGTAGGGTAGAATTACCA
41970762 TTTTACCCCT
Statistics
Matches: 164, Mismatches: 30, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
53 41 0.25
54 123 0.75
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.26
Consensus pattern (54 bp):
AATTACCGAAATACCCTTGTAGGGTAGAATTACCAAAATACCCTTGTAAGGTAG
Found at i:41971184 original size:6 final size:6
Alignment explanation
Indices: 41971175--41971417 Score: 162
Period size: 6 Copynumber: 39.3 Consensus size: 6
41971165 TTGCATTCAC
* *
41971175 ATTCTG ATTCTG ATTCTG -TTACCTG ATACTG ATTCTG ATTCTG TTATCTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG AT-TCTG
* * * *
41971225 ATACTG ATTCTG ATTTTG -TTACCTA ATTCTG ATTCT- AGCTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG A-TTCTG ATTCTG
*
41971274 ATTCTG -TTACCTG ATAT-TG ATTCTG ATTCTG -TTACCTG ATACTG ATTCTG
1 ATTCTG ATT--CTG AT-TCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG
* * *
41971324 ATTCTG -TTACCTA ATTCTG ATTCTG ATTCTG ATTTTG ATTCTG -TCACCTG
1 ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG AT--TCTG
* * *
41971374 ATTTTG ATTCTG ATTCTG ATTCTC ATTTTG ATTCT- AGTTCTG AT
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG A-TTCTG AT
41971418 AATGTTTCTT
Statistics
Matches: 186, Mismatches: 26, Indels: 50
0.71 0.10 0.19
Matches are distributed among these distances:
5 14 0.08
6 141 0.76
7 22 0.12
8 8 0.04
9 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.15, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:41971212 original size:25 final size:25
Alignment explanation
Indices: 41971178--41971260 Score: 130
Period size: 25 Copynumber: 3.3 Consensus size: 25
41971168 CATTCACATT
41971178 CTGATTCTGATTCTGTTACCTGATA
1 CTGATTCTGATTCTGTTACCTGATA
*
41971203 CTGATTCTGATTCTGTTATCTGATA
1 CTGATTCTGATTCTGTTACCTGATA
* * *
41971228 CTGATTCTGATTTTGTTACCTAATT
1 CTGATTCTGATTCTGTTACCTGATA
41971253 CTGATTCT
1 CTGATTCT
41971261 AGCTCTGATT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 53 1.00
ACGTcount: A:0.19, C:0.18, G:0.14, T:0.48
Consensus pattern (25 bp):
CTGATTCTGATTCTGTTACCTGATA
Found at i:41971296 original size:25 final size:25
Alignment explanation
Indices: 41971266--41971354 Score: 144
Period size: 25 Copynumber: 3.6 Consensus size: 25
41971256 ATTCTAGCTC
41971266 TGATTCTGATTCTGTTACCTGATAT
1 TGATTCTGATTCTGTTACCTGATAT
*
41971291 TGATTCTGATTCTGTTACCTGATAC
1 TGATTCTGATTCTGTTACCTGATAT
*
41971316 TGATTCTGATTCTGTTACCTAAT-T
1 TGATTCTGATTCTGTTACCTGATAT
41971340 CTGATTCTGATTCTG
1 -TGATTCTGATTCTG
41971355 ATTTTGATTC
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
25 60 1.00
ACGTcount: A:0.19, C:0.18, G:0.16, T:0.47
Consensus pattern (25 bp):
TGATTCTGATTCTGTTACCTGATAT
Found at i:41971300 original size:62 final size:62
Alignment explanation
Indices: 41971203--41971322 Score: 195
Period size: 62 Copynumber: 1.9 Consensus size: 62
41971193 TTACCTGATA
* * *
41971203 CTGATTCTGATTCTGTTATCTGATACTGATTCTGATTTTGTTACCTAATTCTGATTCTAGCT
1 CTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGTTACCTAATACTGATTCTAGCT
* *
41971265 CTGATTCTGATTCTGTTACCTGATATTGATTCTGATTCTGTTACCTGATACTGATTCT
1 CTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGTTACCTAATACTGATTCT
41971323 GATTCTGTTA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 53 1.00
ACGTcount: A:0.19, C:0.18, G:0.15, T:0.47
Consensus pattern (62 bp):
CTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGTTACCTAATACTGATTCTAGCT
Found at i:41971315 original size:87 final size:87
Alignment explanation
Indices: 41971177--41971391 Score: 351
Period size: 87 Copynumber: 2.5 Consensus size: 87
41971167 GCATTCACAT
* * *
41971177 TCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGTTATCTGATACTGATTCTGATTTT
1 TCTGATTCTGATTCTGTTACCTGATATTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCT
41971242 GTTACCTAATTCTGATTCT-AGC
66 GTTACCTAATTCTGATTCTGA-C
41971264 TCTGATTCTGATTCTGTTACCTGATATTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCT
1 TCTGATTCTGATTCTGTTACCTGATATTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCT
*
41971329 GTTACCTAATTCTGATTCTGAT
66 GTTACCTAATTCTGATTCTGAC
* * *
41971351 TCTGATTTTGATTCTGTCACCTGATTTTGATTCTGATTCTG
1 TCTGATTCTGATTCTGTTACCTGATATTGATTCTGATTCTG
41971392 ATTCTCATTT
Statistics
Matches: 120, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
87 119 0.99
88 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.15, T:0.48
Consensus pattern (87 bp):
TCTGATTCTGATTCTGTTACCTGATATTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCT
GTTACCTAATTCTGATTCTGAC
Found at i:41973525 original size:20 final size:20
Alignment explanation
Indices: 41973500--41973546 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
41973490 TGTGGGTAGG
41973500 CCCGTGTGACTTGGGACACA
1 CCCGTGTGACTTGGGACACA
*
41973520 CCCGTGTGACTTGGGACACG
1 CCCGTGTGACTTGGGACACA
41973540 CCCGTGT
1 CCCGTGT
41973547 CCTCATCCCG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.15, C:0.32, G:0.32, T:0.21
Consensus pattern (20 bp):
CCCGTGTGACTTGGGACACA
Found at i:41975125 original size:33 final size:33
Alignment explanation
Indices: 41975087--41975157 Score: 142
Period size: 33 Copynumber: 2.2 Consensus size: 33
41975077 CGTCTAACTA
41975087 GTTCACAATGTCATTCTCATTGACCATAATATC
1 GTTCACAATGTCATTCTCATTGACCATAATATC
41975120 GTTCACAATGTCATTCTCATTGACCATAATATC
1 GTTCACAATGTCATTCTCATTGACCATAATATC
41975153 GTTCA
1 GTTCA
41975158 TACGCTCATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.37
Consensus pattern (33 bp):
GTTCACAATGTCATTCTCATTGACCATAATATC
Found at i:41977444 original size:48 final size:47
Alignment explanation
Indices: 41977389--41977551 Score: 156
Period size: 48 Copynumber: 3.5 Consensus size: 47
41977379 CCCATAATAA
*
41977389 GATGCCAACGCCATATCCCGGATATGGTCTTACATGGGATCACCACTC
1 GATGCCAACGCCATATCCCAGATATGGTCTTACATGGGATCACCA-TC
* * * * * * *
41977437 GATGCCAATGACGTGTCCCAAACATGGTCTTACATGGGATC-TCAT-
1 GATGCCAACGCCATATCCCAGATATGGTCTTACATGGGATCACCATC
** * *
41977482 -AT--CAACGCCATATCCCAGATATGGTCTTACATGATAACACATATC
1 GATGCCAACGCCATATCCCAGATATGGTCTTACATGGGATCAC-CATC
*
41977527 GATGCCAATGCCATATCCCAGATAT
1 GATGCCAACGCCATATCCCAGATAT
41977552 AATCTTATAA
Statistics
Matches: 89, Mismatches: 20, Indels: 12
0.74 0.17 0.10
Matches are distributed among these distances:
42 27 0.30
44 4 0.04
46 3 0.03
47 2 0.02
48 53 0.60
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (47 bp):
GATGCCAACGCCATATCCCAGATATGGTCTTACATGGGATCACCATC
Found at i:41977558 original size:90 final size:89
Alignment explanation
Indices: 41977394--41977571 Score: 214
Period size: 90 Copynumber: 2.0 Consensus size: 89
41977384 AATAAGATGC
* * * * *
41977394 CAACGCCATATCCCGGATATGGTCTTACATGGGATCACCACTCGATGCCAATGACGTGTCCCAAA
1 CAACGCCATATCCCAGATATGGTCTTACAT-GGATAACCAATCGATGCCAATGACATATCCCAAA
** *
41977459 CATGGTCTTACATGGGATCTCATAT
65 CATAATCTTACAAGGGATCTCATAT
* *
41977484 CAACGCCATATCCCAGATATGGTCTTACAT-GATAACACATATCGATGCCAATGCCATATCCCAG
1 CAACGCCATATCCCAGATATGGTCTTACATGGATAAC-CA-ATCGATGCCAATGACATATCCCAA
* *
41977548 ATATAATCTTATAAGGGATCTCAT
64 ACATAATCTTACAAGGGATCTCAT
41977572 TAACCTGAAT
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
88 5 0.07
89 2 0.03
90 67 0.91
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.26
Consensus pattern (89 bp):
CAACGCCATATCCCAGATATGGTCTTACATGGATAACCAATCGATGCCAATGACATATCCCAAAC
ATAATCTTACAAGGGATCTCATAT
Found at i:41979734 original size:37 final size:37
Alignment explanation
Indices: 41979684--41979762 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
41979674 TTATTACGAA
* * * *
41979684 GTCTTACCTGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
41979721 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
41979758 GTCTT
1 GTCTT
41979763 TAGAGCTCGA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:41979958 original size:47 final size:47
Alignment explanation
Indices: 41979880--41980220 Score: 520
Period size: 47 Copynumber: 7.2 Consensus size: 47
41979870 CCCTTCGGGA
* * * * * **
41979880 CTTATCACATTTATGCACTTTCACATCCATCACATTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
* *
41979927 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
**
41979974 CTTATCACGCATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
*
41980021 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAAGC
*
41980070 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
*
41980117 CCTATTCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTA-TCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
*
41980165 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
41980212 CTTATCACA
1 CTTATCACA
41980221 ATTTAGAATT
Statistics
Matches: 271, Mismatches: 20, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
47 182 0.67
48 45 0.17
49 44 0.16
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.31
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
Found at i:41984164 original size:27 final size:27
Alignment explanation
Indices: 41984127--41984245 Score: 161
Period size: 27 Copynumber: 4.4 Consensus size: 27
41984117 ACTTAGGGGC
* *
41984127 AAAATAGTCATCTTACCACATATGGGA
1 AAAATAGTCATTTTACCACATAAGGGA
41984154 AAAATAGTCATTTTACCACATAAGGGA
1 AAAATAGTCATTTTACCACATAAGGGA
*
41984181 AAAATTA-TCATTTTACC-CATAAGGGC
1 AAAA-TAGTCATTTTACCACATAAGGGA
* * *
41984207 AAAATTGTCATTTCACCATATAAGGGA
1 AAAATAGTCATTTTACCACATAAGGGA
41984234 AAAATAGTCATT
1 AAAATAGTCATT
41984246 CTATTGTTTA
Statistics
Matches: 81, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
25 1 0.01
26 21 0.26
27 57 0.70
28 2 0.02
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (27 bp):
AAAATAGTCATTTTACCACATAAGGGA
Found at i:41984245 original size:53 final size:54
Alignment explanation
Indices: 41984127--41984245 Score: 161
Period size: 53 Copynumber: 2.2 Consensus size: 54
41984117 ACTTAGGGGC
* * *
41984127 AAAATAGTCATCTTACCACATATGGGAAAAATAGTCATTTTACCACATAAGGGA
1 AAAATAGTCATTTTACCACATAAGGGAAAAATAGTCATTTCACCACATAAGGGA
* * *
41984181 AAAATTA-TCATTTTACC-CATAAGGGCAAAATTGTCATTTCACCATATAAGGGA
1 AAAA-TAGTCATTTTACCACATAAGGGAAAAATAGTCATTTCACCACATAAGGGA
41984234 AAAATAGTCATT
1 AAAATAGTCATT
41984246 CTATTGTTTA
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
52 2 0.04
53 40 0.70
54 13 0.23
55 2 0.04
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (54 bp):
AAAATAGTCATTTTACCACATAAGGGAAAAATAGTCATTTCACCACATAAGGGA
Found at i:41987908 original size:27 final size:27
Alignment explanation
Indices: 41987877--41988052 Score: 237
Period size: 27 Copynumber: 6.6 Consensus size: 27
41987867 TTGTACATAC
* *
41987877 GGCAAAACAATCATCTTACCACATAAG
1 GGCAAAACAGTCATTTTACCACATAAG
* * * *
41987904 GGCAAAATAGTCATTTTGCAACATAAA
1 GGCAAAACAGTCATTTTACCACATAAG
* *
41987931 GGTAAAACAGTCATTTTACCATATAAG
1 GGCAAAACAGTCATTTTACCACATAAG
* *
41987958 GGCAAAAAAGTCATTTTACCATATAA-
1 GGCAAAACAGTCATTTTACCACATAAG
41987984 GGCAAAACAGTCATTTTACCACATAAG
1 GGCAAAACAGTCATTTTACCACATAAG
41988011 GGCAAAACAGTCATTTTACCACATAAG
1 GGCAAAACAGTCATTTTACCACATAAG
* *
41988038 GGTAAAAAAGTCATT
1 GGCAAAACAGTCATT
41988053 CTATCATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
26 24 0.18
27 106 0.82
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.24
Consensus pattern (27 bp):
GGCAAAACAGTCATTTTACCACATAAG
Found at i:41988018 original size:80 final size:81
Alignment explanation
Indices: 41987877--41988052 Score: 248
Period size: 80 Copynumber: 2.2 Consensus size: 81
41987867 TTGTACATAC
* * * *
41987877 GGCAAAACAA-TCATCTTACCACATAAGGGCAAAATAGTCATTTTGCAACATAAAGGTAAAACAG
1 GGCAAAA-AAGTCATTTTACCACATAAGGGCAAAACAGTCATTTTACAACATAAAGGCAAAACAG
*
41987941 TCATTTTACCATATAAG
65 TCATTTTACCACATAAG
* * *
41987958 GGCAAAAAAGTCATTTTACCATATAA-GGCAAAACAGTCATTTTACCACATAAGGGCAAAACAGT
1 GGCAAAAAAGTCATTTTACCACATAAGGGCAAAACAGTCATTTTACAACATAAAGGCAAAACAGT
41988022 CATTTTACCACATAAG
66 CATTTTACCACATAAG
*
41988038 GGTAAAAAAGTCATT
1 GGCAAAAAAGTCATT
41988053 CTATCATTTA
Statistics
Matches: 85, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
80 64 0.75
81 21 0.25
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.24
Consensus pattern (81 bp):
GGCAAAAAAGTCATTTTACCACATAAGGGCAAAACAGTCATTTTACAACATAAAGGCAAAACAGT
CATTTTACCACATAAG
Found at i:41990247 original size:27 final size:27
Alignment explanation
Indices: 41990217--41990357 Score: 111
Period size: 27 Copynumber: 5.2 Consensus size: 27
41990207 AAAGGCTACT
*
41990217 CTTTCATATTTCGCCACAAAGGCATTC
1 CTTTCATATTACGCCACAAAGGCATTC
* * * * *
41990244 CTTTTATAATGCGTCACAAAGGCGTTC
1 CTTTCATATTACGCCACAAAGGCATTC
* ***
41990271 CTTTCATATTGCGTTGCAAAGGCATTC
1 CTTTCATATTACGCCACAAAGGCATTC
* * **
41990298 CTTTTATATTAAGCCACAAAGGTTTTC
1 CTTTCATATTACGCCACAAAGGCATTC
* * * **
41990325 TTTTTATATTACGCCACAATGGTGTTC
1 CTTTCATATTACGCCACAAAGGCATTC
41990352 CTTTCA
1 CTTTCA
41990358 AGGTTCTCCG
Statistics
Matches: 90, Mismatches: 24, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 90 1.00
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (27 bp):
CTTTCATATTACGCCACAAAGGCATTC
Found at i:41993814 original size:39 final size:38
Alignment explanation
Indices: 41993726--41993869 Score: 123
Period size: 39 Copynumber: 3.7 Consensus size: 38
41993716 AATATGCATG
** * **
41993726 ATAT-CTGGAATTATATCCGGACTTAAGCTCTGCAGGCT
1 ATATGCTGGAATTATATCCGGGTTTAA-ATCCACAGGCT
* *
41993764 ATCTACTGGAATTATATCCGGGTTTAAATACCCACAGGCT
1 ATATGCTGGAATTATATCCGGGTTTAAAT--CCACAGGCT
* **
41993804 ATATGC-GGAATTATATCCGGAG-TTAAGGTCCGTAGGCT
1 ATATGCTGGAATTATATCCGG-GTTTAA-ATCCACAGGCT
*
41993842 ATATGCTGGAAATATATCCGGGTTTAAA
1 ATATGCTGGAATTATATCCGGGTTTAAA
41993870 GTCCCGAAGG
Statistics
Matches: 86, Mismatches: 13, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
38 18 0.21
39 55 0.64
40 13 0.15
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (38 bp):
ATATGCTGGAATTATATCCGGGTTTAAATCCACAGGCT
Found at i:42001463 original size:39 final size:39
Alignment explanation
Indices: 42001405--42001540 Score: 161
Period size: 39 Copynumber: 3.5 Consensus size: 39
42001395 AATATGCATG
*
42001405 ATAT-CTGGAATTATATCCGGACTTAAGGTCCGCAGGCT
1 ATATGCTGGAATTATATCCGGAGTTAAGGTCCGCAGGCT
* * *
42001443 ATGTGCTGGAATTATATCCGG-GTTCAA-ATACCCACAGGCT
1 ATATGCTGGAATTATATCCGGAGTT-AAGGT--CCGCAGGCT
* *
42001483 ATATGCTGGAATTCTATCCGGAGTTAAGGTTCGCAGGCT
1 ATATGCTGGAATTATATCCGGAGTTAAGGTCCGCAGGCT
*
42001522 ATATGCTGGAAATATATCC
1 ATATGCTGGAATTATATCC
42001541 AGGTTTAAAG
Statistics
Matches: 81, Mismatches: 11, Indels: 11
0.79 0.11 0.11
Matches are distributed among these distances:
38 6 0.07
39 42 0.52
40 29 0.36
41 4 0.05
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (39 bp):
ATATGCTGGAATTATATCCGGAGTTAAGGTCCGCAGGCT
Found at i:42016898 original size:48 final size:48
Alignment explanation
Indices: 42016841--42016959 Score: 193
Period size: 48 Copynumber: 2.5 Consensus size: 48
42016831 ACACATCTCC
* * *
42016841 TACATATTTCACACTAGCCATTCTGCTTTACCACATATACATATATCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACACATACATATATCA
* *
42016889 TATATATTTCACATTAGCCATTCGGCTTTACCACACATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACACATACATATATCA
42016937 TACATATTTCACATTAGCCATTC
1 TACATATTTCACATTAGCCATTC
42016960 ACACACATAT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 65 1.00
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.36
Consensus pattern (48 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACACATACATATATCA
Found at i:42023643 original size:15 final size:17
Alignment explanation
Indices: 42023612--42023644 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
42023602 CACCATTGCC
42023612 GAAACATAAATAAGAAA
1 GAAACATAAATAAGAAA
42023629 GAAA-ATAAA-AAGAAA
1 GAAACATAAATAAGAAA
42023644 G
1 G
42023645 CTAGGTTTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 5 0.31
17 4 0.25
ACGTcount: A:0.73, C:0.03, G:0.15, T:0.09
Consensus pattern (17 bp):
GAAACATAAATAAGAAA
Found at i:42029061 original size:23 final size:23
Alignment explanation
Indices: 42028830--42029066 Score: 239
Period size: 23 Copynumber: 10.3 Consensus size: 23
42028820 CACTGTAATA
* * * *
42028830 TAGCCAAAGCTATCACTGTATCG
1 TAGCCGAAGCTACCACTATATTG
* *
42028853 TAGCCAAAGCTACCACTGTATTG
1 TAGCCGAAGCTACCACTATATTG
* *
42028876 TAGCAGAAGCTACCACTGAGA-TG
1 TAGCCGAAGCTACCACT-ATATTG
* *
42028899 TAGCCGAAGCTATCACTGAGA-TG
1 TAGCCGAAGCTACCACT-ATATTG
* *
42028922 TAGCCAAAGCTACCACTGTATTG
1 TAGCCGAAGCTACCACTATATTG
*
42028945 TAGCCGAAGCTACCACTGTATTG
1 TAGCCGAAGCTACCACTATATTG
** *
42028968 TAGTTGACGCTACCACTATATTG
1 TAGCCGAAGCTACCACTATATTG
*
42028991 TAGCCGAAGCTACCACTGAGA-TG
1 TAGCCGAAGCTACCACT-ATATTG
*
42029014 TAGCCGAAGCTACCACTGAGA-TG
1 TAGCCGAAGCTACCACT-ATATTG
*
42029037 TAGCCGAAGCTACCAGTATATTG
1 TAGCCGAAGCTACCACTATATTG
42029060 TAGCCGA
1 TAGCCGA
42029067 TAGATTCCTA
Statistics
Matches: 187, Mismatches: 23, Indels: 8
0.86 0.11 0.04
Matches are distributed among these distances:
22 3 0.02
23 181 0.97
24 3 0.02
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (23 bp):
TAGCCGAAGCTACCACTATATTG
Found at i:42029066 original size:69 final size:69
Alignment explanation
Indices: 42028830--42029064 Score: 296
Period size: 69 Copynumber: 3.4 Consensus size: 69
42028820 CACTGTAATA
* * * * *
42028830 TAGCCAAAGCTATCACTGTATCGTAGCCAAAGCTACCACTGTATTGTAGCAGAAGCTACCACTGA
1 TAGCCGAAGCTACCACTATATTGTAGCCAAAGCTACCACTGTATTGTAGCCGAAGCTACCACTGA
42028895 GATG
66 GATG
* *
42028899 TAGCCGAAGCTATCACTGAGA-TGTAGCCAAAGCTACCACTGTATTGTAGCCGAAGCTACCACTG
1 TAGCCGAAGCTACCACT-ATATTGTAGCCAAAGCTACCACTGTATTGTAGCCGAAGCTACCACTG
*
42028963 TA-TTG
65 -AGATG
** * * *
42028968 TAGTTGACGCTACCACTATATTGTAGCCGAAGCTACCACTG-AGATGTAGCCGAAGCTACCACTG
1 TAGCCGAAGCTACCACTATATTGTAGCCAAAGCTACCACTGTA-TTGTAGCCGAAGCTACCACTG
42029032 AGATG
65 AGATG
*
42029037 TAGCCGAAGCTACCAGTATATTGTAGCC
1 TAGCCGAAGCTACCACTATATTGTAGCC
42029065 GATAGATTCC
Statistics
Matches: 143, Mismatches: 18, Indels: 10
0.84 0.11 0.06
Matches are distributed among these distances:
68 4 0.03
69 137 0.96
70 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.24
Consensus pattern (69 bp):
TAGCCGAAGCTACCACTATATTGTAGCCAAAGCTACCACTGTATTGTAGCCGAAGCTACCACTGA
GATG
Found at i:42033663 original size:40 final size:40
Alignment explanation
Indices: 42033590--42033813 Score: 328
Period size: 40 Copynumber: 5.5 Consensus size: 40
42033580 ACCCAAGTAT
* *
42033590 CTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
*
42033629 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
42033669 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
42033709 CTTCGGGACTTAGCCCGGGTATAG-CAACTACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTA---GCACAAATGC
* *
42033752 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
42033792 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
42033814 CATCCGAATA
Statistics
Matches: 170, Mismatches: 8, Indels: 13
0.89 0.04 0.07
Matches are distributed among these distances:
39 12 0.07
40 121 0.71
41 1 0.01
43 36 0.21
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Done.