Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007882.1 Hibiscus syriacus cultivar Beakdansim tig00110260_pilon, whole genome shotgun sequence
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: 1274288
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 5
Found at i:856209 original size:4 final size:4
Alignment explanation
Indices: 856200--856229 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
856190 TGTTATACAT
856200 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
856230 ATCATCACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:865454 original size:39 final size:39
Alignment explanation
Indices: 865411--865507 Score: 176
Period size: 39 Copynumber: 2.5 Consensus size: 39
865401 AAATCTAGCA
*
865411 ATTTATTTCCTTTTACAAGATAGGAAAATAAACCCAATG
1 ATTTATTTCCTTTTACAAAATAGGAAAATAAACCCAATG
*
865450 ATTTATTTCCTTTTACAAAATAGGAAAATAAATCCAATG
1 ATTTATTTCCTTTTACAAAATAGGAAAATAAACCCAATG
865489 ATTTATTTCCTTTTACAAA
1 ATTTATTTCCTTTTACAAA
865508 CCAATATCAT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.38
Consensus pattern (39 bp):
ATTTATTTCCTTTTACAAAATAGGAAAATAAACCCAATG
Found at i:865598 original size:40 final size:40
Alignment explanation
Indices: 865554--865631 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
865544 TTTCTATTAC
* *
865554 AAAATATGAAAATAAATCCAACGATTTAATTCTTTTTATA
1 AAAATAGGAAAATAAATCCAACGATTTAATTCCTTTTATA
* * *
865594 AAAATAGGAAAATAAATTCACCGATTTATTTCCTTTTA
1 AAAATAGGAAAATAAATCCAACGATTTAATTCCTTTTA
865632 CAATTAGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.37
Consensus pattern (40 bp):
AAAATAGGAAAATAAATCCAACGATTTAATTCCTTTTATA
Found at i:865792 original size:58 final size:57
Alignment explanation
Indices: 865603--865967 Score: 194
Period size: 58 Copynumber: 6.4 Consensus size: 57
865593 AAAAATAGGA
* * * * * *
865603 AAATAAATTCACCGATTTATTTCCTTTTAC-AATTAGAATCATATAAGATT-T-ACAGAA
1 AAATAAATTCAACAATTTATTT-CTTTTACAAAATAGAATCATTTAAAATTCTCA-AG-G
* * * * *
865660 AAATAAATTTAACGATTTATTTCTTTTTGCATAACAT-G-ATC-TTTCAAGATTC-CTAAGA
1 AAATAAATTCAACAATTTATTTC-TTTTACA-AA-ATAGAATCATTT-AAAATTCTC-AAGG
*
865718 AAATTAATT-AACCAATTTATTTACTTTTACAAAATAGAATCATTTAAAATTCTCAAGG
1 AAATAAATTCAA-CAATTTATTT-CTTTTACAAAATAGAATCATTTAAAATTCTCAAGG
* *
865776 AAATAAATTCAACAATTTATTT-TCCTTACAAAATTAGAATCATTCAAGAA-TCTCAAGG
1 AAATAAATTCAACAATTTATTTCT-TTTACAAAA-TAGAATCATTTAA-AATTCTCAAGG
*** *
865834 AAATAAATTCAGTTATTTATTTTTCTTTAC--AA-AG------TTAAAGATTCTCAAGG
1 AAATAAATTCAACAATTTATTTCT-TTTACAAAATAGAATCATTTAAA-ATTCTCAAGG
* * ** * * *
865884 AAATAAATTCAACTATTTATTT-TCCTTACAATGTTAGAATTATTCAACATTCTCAAGG
1 AAATAAATTCAACAATTTATTTCT-TTTACAA-AATAGAATCATTTAAAATTCTCAAGG
*
865942 AAATAAATTCAACAAATTTTTTTCTT
1 AAATAAATTCAAC-AATTTATTTCTT
865968 ACGAAGTTAG
Statistics
Matches: 247, Mismatches: 28, Indels: 64
0.73 0.08 0.19
Matches are distributed among these distances:
48 1 0.00
49 10 0.04
50 28 0.11
53 2 0.01
55 2 0.01
56 4 0.02
57 42 0.17
58 125 0.51
59 30 0.12
60 3 0.01
ACGTcount: A:0.41, C:0.13, G:0.07, T:0.39
Consensus pattern (57 bp):
AAATAAATTCAACAATTTATTTCTTTTACAAAATAGAATCATTTAAAATTCTCAAGG
Found at i:865884 original size:50 final size:49
Alignment explanation
Indices: 865821--865919 Score: 144
Period size: 50 Copynumber: 2.0 Consensus size: 49
865811 AGAATCATTC
** *
865821 AAGAATCTCAAGGAAATAAATTCAGTTATTTATTTTTCTTTACAAAGTTA
1 AAGAATCTCAAGGAAATAAATTCAACTATTTA-TTTTCCTTACAAAGTTA
* *
865871 AAGATTCTCAAGGAAATAAATTCAACTATTTATTTTCCTTACAATGTTA
1 AAGAATCTCAAGGAAATAAATTCAACTATTTATTTTCCTTACAAAGTTA
865920 GAATTATTCA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
49 15 0.34
50 29 0.66
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.39
Consensus pattern (49 bp):
AAGAATCTCAAGGAAATAAATTCAACTATTTATTTTCCTTACAAAGTTA
Found at i:865994 original size:58 final size:58
Alignment explanation
Indices: 865766--865994 Score: 194
Period size: 58 Copynumber: 4.1 Consensus size: 58
865756 ATCATTTAAA
** * **
865766 ATTCTCAAGGAAATAAATTCAACAATTTATTTTCCTTACAAAATTAGAATCATTCAAG
1 ATTCTCAAGGAAATAAATTCAACAATTTATTTTCCTTACAATGTTAGAATAACGCAAG
* *** * *
865824 AATCTCAAGGAAATAAATTCAGTTATTTATTTTTCTTTACAA----AG--TTA---AAG
1 ATTCTCAAGGAAATAAATTCAACAATTTA-TTTTCCTTACAATGTTAGAATAACGCAAG
* * ** *
865874 ATTCTCAAGGAAATAAATTCAACTATTTATTTTCCTTACAATGTTAGAATTATTCAAC
1 ATTCTCAAGGAAATAAATTCAACAATTTATTTTCCTTACAATGTTAGAATAACGCAAG
865932 ATTCTCAAGGAAATAAATTCAACAAATTT-TTTT-CTTACGAA-GTTAGAATCAACGCAAG
1 ATTCTCAAGGAAATAAATTCAAC-AATTTATTTTCCTTAC-AATGTTAGAAT-AACGCAAG
865990 ATTCT
1 ATTCT
865995 AACGATGAAA
Statistics
Matches: 142, Mismatches: 16, Indels: 26
0.77 0.09 0.14
Matches are distributed among these distances:
49 11 0.08
50 29 0.20
53 4 0.03
55 5 0.04
57 13 0.09
58 65 0.46
59 15 0.11
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (58 bp):
ATTCTCAAGGAAATAAATTCAACAATTTATTTTCCTTACAATGTTAGAATAACGCAAG
Found at i:866365 original size:45 final size:45
Alignment explanation
Indices: 866150--866366 Score: 231
Period size: 45 Copynumber: 4.8 Consensus size: 45
866140 ACCAATCCAT
* * *
866150 TAATCGAAAGGAACTAATCCTTTGATTTTAATTTTCGCAA-TCCAG
1 TAATCGAAAGGAACTAATCATTTGATTTTAATTTTGGCAACT-CAA
* * * * * *
866195 TAATTGAAAGAAACTAATCCTTCGATTTTAATTTTTGCATCTCAA
1 TAATCGAAAGGAACTAATCATTTGATTTTAATTTTGGCAACTCAA
* *
866240 TAATCGACAGGAAATAATCCA-TTGATTTTAATTTTGGCAACTCAA
1 TAATCGAAAGGAACTAAT-CATTTGATTTTAATTTTGGCAACTCAA
* * ** *
866285 TAATCAAAAGAAACTAATCATTTGATTTTGTTTTTGGCAACACAA
1 TAATCGAAAGGAACTAATCATTTGATTTTAATTTTGGCAACTCAA
* * *
866330 TAATCAAAAGGAACTAATAATTTGATTTTACTTTTGG
1 TAATCGAAAGGAACTAATCATTTGATTTTAATTTTGG
866367 TAATGTAATA
Statistics
Matches: 144, Mismatches: 25, Indels: 6
0.82 0.14 0.03
Matches are distributed among these distances:
44 2 0.01
45 140 0.97
46 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (45 bp):
TAATCGAAAGGAACTAATCATTTGATTTTAATTTTGGCAACTCAA
Found at i:873130 original size:55 final size:52
Alignment explanation
Indices: 873054--873687 Score: 706
Period size: 55 Copynumber: 11.7 Consensus size: 52
873044 TGGGTTCGCT
* * *
873054 CCCTATTTCTTTAGAGGGTATAAGACTTGAATC-ATCTTCAACAAACTTGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGAC-TCAA-CAATCTTCAAC-AA-TTGTCTGCC
* * * *
873109 CCCTATTTCTTCAGAGAGTATAAGAC-CCATAATCTTCATCAATCGCATCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCAACAATCTTCAACAATTG--TCTGCC
*
873162 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTC-AACAATCTTCAACAATT--GTCTGCC
* *
873217 CCCTATTTCTTCAGAGAGTATAAGAC-CAACAATCTTCATCAATCGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCAACAATCTTCAACAAT--TGTCTGCC
*
873270 CCCTATTTCTTCAGAGAGTATAAGA-TCCAAACAATCTTCAACGATTGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACT-C-AACAATCTTCAACAATT--GTCTGCC
* * *
873325 CCCTATTTCTTCAGAGAGTATAAGAC-CCACAATCTTCATCAATCGCATCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCAACAATCTTCAACAATTG--TCTGCC
*
873378 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGTGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTC-AACAATCTTCAAC-AAT-TGTCTGCC
* *
873433 CCCTATTTCTTCAGAGAGTATAAGAC-CCACAATCTTCATCAATTGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCAACAATCTTCAACAATT--GTCTGCC
*
873486 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTC-AACAATCTTCAACAATT--GTCTGCC
* *
873541 CTCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTC-AACAATCTTCAACAATT--GTCTGCC
* * * * *
873596 CCCTATTTCTTTAGAGAGTATAAGAC-CCACAATATTCATCAATCGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCAACAATCTTCAACAAT--TGTCTGCC
*
873649 CCCTATTTCTTCAGAGAGTATAAGACCCGAACAATCTTC
1 CCCTATTTCTTCAGAGAGTATAAGACTC-AACAATCTTC
873688 TTTTACTTCA
Statistics
Matches: 507, Mismatches: 43, Indels: 58
0.83 0.07 0.10
Matches are distributed among these distances:
51 4 0.01
52 4 0.01
53 220 0.43
54 9 0.02
55 266 0.52
56 2 0.00
57 2 0.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (52 bp):
CCCTATTTCTTCAGAGAGTATAAGACTCAACAATCTTCAACAATTGTCTGCC
Found at i:873183 original size:108 final size:107
Alignment explanation
Indices: 873054--873687 Score: 918
Period size: 108 Copynumber: 5.9 Consensus size: 107
873044 TGGGTTCGCT
* * * *
873054 CCCTATTTCTTTAGAGGGTATAAGACTTGAATC-ATCTTCAACAAACTT-GTCTGCCCCCTATTT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAA-CAATCTTCAAC-GA-TTCGTCTGCCCCCTATTT
* *
873117 CTTCAGAGAGTATAAGACCCATAATCTTCATCAATCGCATCTGCC
63 CTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCC
873162 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATT-CGTCTGCCCCCTATTTCT
*
873227 TCAGAGAGTATAAGACCAACAATCTTCATCAATCGCGTCTGCC
65 TCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCC
*
873270 CCCTATTTCTTCAGAGAGTATAAGA-TCCAAACAATCTTCAACGATTGCGTCTGCCCCCTATTTC
1 CCCTATTTCTTCAGAGAGTATAAGACT-CGAACAATCTTCAACGATT-CGTCTGCCCCCTATTTC
*
873334 TTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCATCTGCC
64 TTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCC
*
873378 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGTGTCTGCCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATT-CGTCTGCCCCCTATTTCT
*
873443 TCAGAGAGTATAAGACCCACAATCTTCATCAATTGCGTCTGCC
65 TCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCC
*
873486 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCTCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATT-CGTCTGCCCCCTATTTCT
* * * *
873551 TCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCC
65 TCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCGTCTGCC
* * * * * *
873596 CCCTATTTCTTTAGAGAGTATAAGAC-C-CACAATATTCATCAATCGCGTCTGCCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGAT-TCGTCTGCCCCCTATTTCT
873659 TCAGAGAGTATAAGACCCGAACAATCTTC
65 TCAGAGAGTATAAGACCC--ACAATCTTC
873688 TTTTACTTCA
Statistics
Matches: 489, Mismatches: 27, Indels: 20
0.91 0.05 0.04
Matches are distributed among these distances:
106 2 0.00
107 4 0.01
108 432 0.88
109 3 0.01
110 48 0.10
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (107 bp):
CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTCGTCTGCCCCCTATTTCTT
CAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCC
Found at i:873329 original size:163 final size:163
Alignment explanation
Indices: 873054--873687 Score: 958
Period size: 163 Copynumber: 3.9 Consensus size: 163
873044 TGGGTTCGCT
* * * *
873054 CCCTATTTCTTTAGAGGGTATAAGACTTGAATC-ATCTTCAACAAACTT--GTCTGCCCCCTATT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAA-CAATCTTCAAC-GA-TTGCGTCTGCCCCCTATT
* *
873116 TCTTCAGAGAGTATAAGACCCATAATCTTCATCAATCGCATCTGCCCCCTATTTCTTCAGAGAGT
63 TCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGT
873181 ATAAGACTCGAACAATCTTCAACGATTGCGTCTGCC
128 ATAAGACTCGAACAATCTTCAACGATTGCGTCTGCC
* * *
873217 CCCTATTTCTTCAGAGAGTATAAGAC-C-AACAATCTTCATCAATCGCGTCTGCCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCT
* * * *
873280 TCAGAGAGTATAAGATCCAAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCTTCAGAGAGTA
66 TCAGAGAGTATAAGA-CC-CACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTA
* * * * *
873345 TAAGAC-C-CACAATCTTCATCAATCGCATCTGCC
129 TAAGACTCGAACAATCTTCAACGATTGCGTCTGCC
*
873378 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGTGTCTGCCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCT
*
873443 TCAGAGAGTATAAGACCCACAATCTTCATCAATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATA
66 TCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATA
873508 AGACTCGAACAATCTTCAACGATTGCGTCTGCC
131 AGACTCGAACAATCTTCAACGATTGCGTCTGCC
*
873541 CTCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCT
* *
873606 TTAGAGAGTATAAGACCCACAATATTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATA
66 TCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATA
*
873671 AGACCCGAACAATCTTC
131 AGACTCGAACAATCTTC
873688 TTTTACTTCA
Statistics
Matches: 428, Mismatches: 34, Indels: 18
0.89 0.07 0.04
Matches are distributed among these distances:
159 1 0.00
160 3 0.01
161 138 0.32
162 7 0.02
163 279 0.65
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (163 bp):
CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCT
TCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATA
AGACTCGAACAATCTTCAACGATTGCGTCTGCC
Found at i:874744 original size:128 final size:127
Alignment explanation
Indices: 874465--874869 Score: 573
Period size: 128 Copynumber: 3.2 Consensus size: 127
874455 ATCATGATGC
* *
874465 GGGTTCAGTCGTGCCCCAACATTATCTTATACTGGTACGGGCCTTTCAAAATGCCCTTATTACCT
1 GGGTTCAGTCGTGCCCCAACATTATCTTATACTGGTACGGGCC-TTCAAAATGCCC-CATCACCT
* ** * *
874530 CAAATTGTAAGGCTCATTCTTCATGCC-TC--CTTGGTCTGAATCTTTTCATCTCAACATGATGT
64 CAGATTGTAAGGCTCATTCTTCATGCCTTCTTCTTCTTCTGAAT-TTTTCATCTCAACCTAATGT
*
874592 GGGTTCAGTCGTGCCCCAACATTATCTTATACTGGTACGGGCCTTCAAAATGCCCCATCACCTTA
1 GGGTTCAGTCGTGCCCCAACATTATCTTATACTGGTACGGGCCTTCAAAATGCCCCATCACCTCA
*
874657 GTTTGTAAGGCTCATTCTTCATGCCTTCTTCTTCTTCTGAATTTTATCATCTCAACCTAATGT
66 GATTGTAAGGCTCATTCTTCATGCCTTCTTCTTCTTCTGAATTTT-TCATCTCAACCTAATGT
* * * **
874720 GGGTTCAGTCATGCCCCAACATTATCTTGTACTGGTACGAGCCTTCAAAATATCCCATCACCTCA
1 GGGTTCAGTCGTGCCCCAACATTATCTTATACTGGTACGGGCCTTCAAAATGCCCCATCACCTCA
* * *
874785 GATTGTAAGGCTTATTCTTCATGCCTTCTTCTTCTTCTAAATCTTGTCATCTCAACCTAATGT
66 GATTGTAAGGCTCATTCTTCATGCCTTCTTCTTCTTCTGAAT-TTTTCATCTCAACCTAATGT
* *
874848 GGGTTCAGCCGTGCCACAACAT
1 GGGTTCAGTCGTGCCCCAACAT
874870 ATCGCAACTT
Statistics
Matches: 251, Mismatches: 22, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
125 30 0.12
126 14 0.06
127 46 0.18
128 159 0.63
129 2 0.01
ACGTcount: A:0.22, C:0.27, G:0.16, T:0.35
Consensus pattern (127 bp):
GGGTTCAGTCGTGCCCCAACATTATCTTATACTGGTACGGGCCTTCAAAATGCCCCATCACCTCA
GATTGTAAGGCTCATTCTTCATGCCTTCTTCTTCTTCTGAATTTTTCATCTCAACCTAATGT
Found at i:876129 original size:16 final size:16
Alignment explanation
Indices: 876111--876140 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
876101 TTCATTCTTT
876111 TTTTC-ATTTTTCTCA
1 TTTTCAATTTTTCTCA
876126 TTTTCAATTTTTCTC
1 TTTTCAATTTTTCTC
876141 TTTCTTTTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.13, C:0.20, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTCAATTTTTCTCA
Found at i:876167 original size:6 final size:6
Alignment explanation
Indices: 876110--876203 Score: 52
Period size: 6 Copynumber: 15.2 Consensus size: 6
876100 TTTCATTCTT
* *
876110 TTTTTC ATTTTTC TCATTTTC AATTTTTC TCTTTC TTTTCC TTTTT- TATTTTC
1 TTTTTC -TTTTTC T--TTTTC --TTTTTC TTTTTC TTTTTC TTTTTC T-TTTTC
* * *
876163 TTTTTC -ATTTC ATTTTT- TTTATC -TTTTC TTTTTC TCTTTC T
1 TTTTTC TTTTTC -TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC T
876204 ATATTTCTCT
Statistics
Matches: 68, Mismatches: 9, Indels: 21
0.69 0.09 0.21
Matches are distributed among these distances:
5 13 0.19
6 34 0.50
7 10 0.15
8 10 0.15
10 1 0.01
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (6 bp):
TTTTTC
Found at i:885399 original size:13 final size:13
Alignment explanation
Indices: 885377--885417 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
885367 GACGCGCAAT
*
885377 ATGCACGTCATAA
1 ATGCGCGTCATAA
*
885390 ATGCGTGTCATAA
1 ATGCGCGTCATAA
885403 ATGCGCGTCATAA
1 ATGCGCGTCATAA
885416 AT
1 AT
885418 TTATGACGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.27
Consensus pattern (13 bp):
ATGCGCGTCATAA
Found at i:885487 original size:100 final size:100
Alignment explanation
Indices: 885296--885480 Score: 219
Period size: 100 Copynumber: 1.9 Consensus size: 100
885286 CGCAATGTAA
* * * * * *
885296 GTCATAAATACGTGTCATAAATTTATGATACACAAATGTGTGTCATCTTCATTTATGACGGGGGC
1 GTCATAAATACGCGTCATAAATTTATGACACACAAATGCGCGTCATCTTAATTCATGACGGGGGC
* **
885361 TTCAATGACGCGCAATATGCACGTCATAAATGCGT
66 TTCAACGACAAGCAATATGCACGTCATAAATGCGT
* * ** * *
885396 GTCATAAATGCGCGTCATAAATTTATGACGCACAGTTGCGCGTCATCTTAAATTCATGTCGGTGG
1 GTCATAAATACGCGTCATAAATTTATGACACACAAATGCGCGTCATCTT-AATTCATGACGGGGG
885461 CTTCAACGACAAGCAA-ATGC
65 CTTCAACGACAAGCAATATGC
885481 GTGTCATCCG
Statistics
Matches: 69, Mismatches: 15, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
100 45 0.65
101 24 0.35
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (100 bp):
GTCATAAATACGCGTCATAAATTTATGACACACAAATGCGCGTCATCTTAATTCATGACGGGGGC
TTCAACGACAAGCAATATGCACGTCATAAATGCGT
Found at i:888561 original size:24 final size:25
Alignment explanation
Indices: 888534--888580 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
888524 TAACATGTTT
888534 AAAAAT-AAAACTT-AAAAGAAAAG
1 AAAAATGAAAACTTGAAAAGAAAAG
888557 AAAAATGAAAACTTGAAAAGAAAA
1 AAAAATGAAAACTTGAAAAGAAAA
888581 TAAAGGAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 6 0.27
24 7 0.32
25 9 0.41
ACGTcount: A:0.72, C:0.04, G:0.11, T:0.13
Consensus pattern (25 bp):
AAAAATGAAAACTTGAAAAGAAAAG
Found at i:894463 original size:32 final size:31
Alignment explanation
Indices: 894397--894472 Score: 73
Period size: 32 Copynumber: 2.4 Consensus size: 31
894387 TAACAATAAT
* *
894397 ATGTCTAAGTTTACTTTAAAAGATGAACACC
1 ATGTCCAAATTTACTTTAAAAGATGAACACC
* * *
894428 ATGTTCAAATTTACTTATAAAAAGATGGA-AGC
1 ATGTCCAAATTTACTT-T-AAAAGATGAACACC
*
894460 ATGTCCAATTTTA
1 ATGTCCAAATTTA
894473 TAAAAGATAG
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
31 13 0.36
32 14 0.39
33 9 0.25
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.34
Consensus pattern (31 bp):
ATGTCCAAATTTACTTTAAAAGATGAACACC
Found at i:895623 original size:36 final size:36
Alignment explanation
Indices: 895573--895672 Score: 114
Period size: 36 Copynumber: 2.8 Consensus size: 36
895563 AGATGAAGTT
* * *
895573 GAAAAGATATAATAAAATAAATAATTATAATTTAAAAA
1 GAAAA-AT-TAATAAAATAAATAATAATAAATAAAAAA
895611 GAAAAATTAATAAAATAAATAATAATAAATAAAAAA
1 GAAAAATTAATAAAATAAATAATAATAAATAAAAAA
* *
895647 GGAAAA-CAATAAAAT-AATAAATAATA
1 GAAAAATTAATAAAATAAAT-AATAATA
895673 GTAGTAAAGA
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
34 3 0.05
35 15 0.27
36 31 0.55
37 2 0.04
38 5 0.09
ACGTcount: A:0.70, C:0.01, G:0.05, T:0.24
Consensus pattern (36 bp):
GAAAAATTAATAAAATAAATAATAATAAATAAAAAA
Found at i:903268 original size:24 final size:23
Alignment explanation
Indices: 903233--903279 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
903223 GATTATCATG
903233 GCATCTTCAAATATTGGAAAGATT
1 GCATCTTCAAATATTGG-AAGATT
* *
903257 GCATCTTGAAATGTTGGAAGATT
1 GCATCTTCAAATATTGGAAGATT
903280 ATGATCTAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (23 bp):
GCATCTTCAAATATTGGAAGATT
Found at i:914549 original size:26 final size:26
Alignment explanation
Indices: 914520--914608 Score: 160
Period size: 26 Copynumber: 3.4 Consensus size: 26
914510 GAGGGAATGA
*
914520 CGAGCTAGGCGTTCGAGAGGAGCTAG
1 CGAGCTAGGCGTTCGAGAGAAGCTAG
914546 CGAGCTAGGCGTTCGAGAGAAGCTAG
1 CGAGCTAGGCGTTCGAGAGAAGCTAG
914572 CGAGCTAGGCGTTCGAGAGAAGCTAG
1 CGAGCTAGGCGTTCGAGAGAAGCTAG
914598 CGAGCTGAGGC
1 CGAGCT-AGGC
914609 AATTTGTGGT
Statistics
Matches: 61, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
26 57 0.93
27 4 0.07
ACGTcount: A:0.25, C:0.20, G:0.40, T:0.15
Consensus pattern (26 bp):
CGAGCTAGGCGTTCGAGAGAAGCTAG
Found at i:921532 original size:21 final size:20
Alignment explanation
Indices: 921506--921603 Score: 83
Period size: 21 Copynumber: 4.8 Consensus size: 20
921496 ATCAGTTTCC
921506 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
**
921527 AAAATCGCAACGCGATAGT-
1 AAAATCGCAACGCGATTTTG
**
921546 ACAAATTCGCATTGCGATTTT-
1 A-AAA-TCGCAACGCGATTTTG
* *
921567 ACAGAATCGCAACGCGAATATG
1 A-A-AATCGCAACGCGATTTTG
921589 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
921604 ACACATAAAT
Statistics
Matches: 63, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
19 1 0.02
20 17 0.27
21 42 0.67
22 3 0.05
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.20
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:921596 original size:20 final size:20
Alignment explanation
Indices: 921571--921763 Score: 194
Period size: 20 Copynumber: 9.6 Consensus size: 20
921561 GATTTTACAG
* **
921571 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGAA
*
921591 AATCGCAACGCG-AACAC-ATA
1 AATCGCAACGCGTATC-CGA-A
*
921611 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGAA
* *
921631 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGAA
*
921651 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGAA
* *
921671 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGAA
* *
921691 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGAA
* *
921711 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCG-AA
*
921732 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGAA
921752 AATCGCAACGCG
1 AATCGCAACGCG
921764 ATTTTTAAAG
Statistics
Matches: 149, Mismatches: 17, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
19 2 0.01
20 129 0.87
21 18 0.12
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGAA
Found at i:921634 original size:40 final size:39
Alignment explanation
Indices: 921571--921764 Score: 228
Period size: 40 Copynumber: 4.8 Consensus size: 39
921561 GATTTTACAG
* ** * *
921571 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CGTA
* *
921611 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCGTA
* *
921651 AATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCGTA
* *
921691 TATCGCAACGCGTATCCGTAAATCGCAACGAC-AATACGTAA
1 AATCGCAACGCGTATCCGTAAATCGCAACG-CGAA-CCGT-A
921732 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
921765 TTTTTAAAGC
Statistics
Matches: 135, Mismatches: 14, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
39 1 0.01
40 100 0.74
41 34 0.25
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (39 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACCGTA
Found at i:921656 original size:60 final size:60
Alignment explanation
Indices: 921571--921763 Score: 255
Period size: 60 Copynumber: 3.2 Consensus size: 60
921561 GATTTTACAG
* ** * *
921571 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACGTAAATCGCAACGCGTATCCGTA
* * *
921631 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATC-CGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACACGTAAATCGCAACGCGTATCCGTA
* *
921691 TATCGCAACGCGTATCCGTAAATCGCAACGAC-AATACGTAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACG-CGAACACGT-AAATCGCAACGCGTATCCGTA
921752 AATCGCAACGCG
1 AATCGCAACGCG
921764 ATTTTTAAAG
Statistics
Matches: 115, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
59 1 0.01
60 80 0.70
61 34 0.30
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACGTAAATCGCAACGCGTATCCGTA
Found at i:922182 original size:33 final size:33
Alignment explanation
Indices: 922143--922213 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
922133 TTCACTTAGA
*
922143 TTTCATTTCGCGTTACGATTCTCTTGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
922176 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
922209 TTTCA
1 TTTCA
922214 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.17, T:0.49
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:922337 original size:20 final size:20
Alignment explanation
Indices: 922293--922402 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 20
922283 TGCAGAAGAG
*
922293 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
922314 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
922334 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
922355 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
922369 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
922388 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
922403 CGCAACGCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 15 0.21
20 20 0.27
21 23 0.32
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:922350 original size:41 final size:38
Alignment explanation
Indices: 922286--922402 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 38
922276 TTCAATTTGC
* *
922286 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
922324 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
922365 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
922398 AGAAT
1 AGAAT
922403 CGCAACGCGA
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
33 23 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 33 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:922372 original size:14 final size:14
Alignment explanation
Indices: 922353--922409 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
922343 GAGAAATGAA
922353 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
922367 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
922386 AATCGCAACGAGAG
1 AATCGCAACGAGAG
922400 AATCGCAACG
1 AATCGCAACG
922410 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:922385 original size:33 final size:33
Alignment explanation
Indices: 922345--922425 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
922335 CGCAACGAGA
922345 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
922378 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
922411 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
922426 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:922443 original size:19 final size:19
Alignment explanation
Indices: 922421--922548 Score: 87
Period size: 19 Copynumber: 7.1 Consensus size: 19
922411 GAAACCAAAA
*
922421 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
922440 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
922454 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
922473 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
922487 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
922507 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
922527 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
922547 TC
1 TC
922549 AACCAAAAGA
Statistics
Matches: 87, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
14 20 0.23
16 6 0.07
17 6 0.07
19 22 0.25
20 19 0.22
21 14 0.16
ACGTcount: A:0.11, C:0.25, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:922462 original size:14 final size:14
Alignment explanation
Indices: 922443--922499 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
922433 TTTCATTTCG
922443 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
922457 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
922476 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
922490 CGTTGCGATT
1 CGTTGCGATT
922500 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:922468 original size:33 final size:33
Alignment explanation
Indices: 922426--922548 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
922416 CAAAATCGCA
922426 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
922459 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
922492 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCG
922533 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
922549 AACCAAAAGA
Statistics
Matches: 81, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
33 45 0.56
34 2 0.02
35 6 0.07
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.02
41 21 0.26
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:922510 original size:21 final size:21
Alignment explanation
Indices: 922484--922548 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
922474 CGCGTTGCGA
922484 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
922505 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
922525 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
922546 TTC
1 TTC
922549 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:924392 original size:93 final size:93
Alignment explanation
Indices: 924233--924608 Score: 700
Period size: 93 Copynumber: 4.1 Consensus size: 93
924223 TAGATTGCTT
*
924233 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
924298 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
924326 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAAGAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
924391 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
924419 AGTAAATTTGTTCGGTTGATGCCAATTCTGCTAAACTGTGTAGTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
924484 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
924512 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAATTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
924577 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
924604 AGTAA
1 AGTAA
924609 TGCAATCCAT
Statistics
Matches: 275, Mismatches: 8, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
92 6 0.02
93 269 0.98
ACGTcount: A:0.22, C:0.12, G:0.20, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:924712 original size:19 final size:19
Alignment explanation
Indices: 924688--924765 Score: 94
Period size: 19 Copynumber: 4.4 Consensus size: 19
924678 GCAACGAGAG
**
924688 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAACCAA
924707 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
924726 AATCGCAA--CG--A-CAA
1 AATCGCAACGCGAAACCAA
*
924740 AATCGCAACGGGAAACCAA
1 AATCGCAACGCGAAACCAA
924759 AATCGCA
1 AATCGCA
924766 TTGCGATTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
14 11 0.22
15 1 0.02
16 1 0.02
17 2 0.04
18 1 0.02
19 35 0.69
ACGTcount: A:0.47, C:0.27, G:0.18, T:0.08
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:924736 original size:52 final size:53
Alignment explanation
Indices: 924656--924765 Score: 150
Period size: 52 Copynumber: 2.1 Consensus size: 53
924646 TAGTTTACTT
* * * **
924656 TCGCAACACGAAACTTAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACACGAAACTCAAAATCGCAACGACAAAATCGCAACGCGAAACCAAAA
* *
924709 TCGCAACGCGAAAC-CAAAATCGCAACGACAAAATCGCAACGGGAAACCAAAA
1 TCGCAACACGAAACTCAAAATCGCAACGACAAAATCGCAACGCGAAACCAAAA
924761 TCGCA
1 TCGCA
924766 TTGCGATTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
52 37 0.74
53 13 0.26
ACGTcount: A:0.46, C:0.26, G:0.18, T:0.09
Consensus pattern (53 bp):
TCGCAACACGAAACTCAAAATCGCAACGACAAAATCGCAACGCGAAACCAAAA
Found at i:924740 original size:14 final size:14
Alignment explanation
Indices: 924723--924749 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
924713 AACGCGAAAC
924723 CAAAATCGCAACGA
1 CAAAATCGCAACGA
924737 CAAAATCGCAACG
1 CAAAATCGCAACG
924750 GGAAACCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.30, G:0.15, T:0.07
Consensus pattern (14 bp):
CAAAATCGCAACGA
Found at i:924783 original size:19 final size:19
Alignment explanation
Indices: 924761--924933 Score: 150
Period size: 19 Copynumber: 9.6 Consensus size: 19
924751 GAAACCAAAA
*
924761 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
924780 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
924794 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
924813 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
924829 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
924846 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* **
924865 TCACGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
924884 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
924903 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
924923 TCGTGTTGCGA
1 TCGCGTTGCGA
924934 AAGTAAACTA
Statistics
Matches: 125, Mismatches: 18, Indels: 21
0.76 0.11 0.13
Matches are distributed among these distances:
14 17 0.14
16 8 0.06
17 8 0.06
19 80 0.64
20 12 0.10
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:924802 original size:14 final size:14
Alignment explanation
Indices: 924783--924839 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
924773 TTTCATTTCG
924783 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
924797 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
*
924814 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTCT
924830 CGTTGCGATT
1 CGTTGCGATT
924840 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
16 7 0.19
17 7 0.19
19 6 0.17
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:924808 original size:33 final size:33
Alignment explanation
Indices: 924766--924858 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
924756 CAAAATCGCA
924766 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
924799 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
924832 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
924859 TTGGTTTCAC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:924891 original size:38 final size:38
Alignment explanation
Indices: 924766--924933 Score: 158
Period size: 33 Copynumber: 4.7 Consensus size: 38
924756 CAAAATCGCA
924766 TTGCGATTTTCATTTCGCGTTGCGATTCTC---T--CG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCATTTCACG
* *
924799 TTGCGATTTTCATTTCGCATTGCGA-T-TC-TGT--CG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCATTTCACG
* **
924832 TTGCGATTTTCATTTCGCGTTGCGATTTTGGTTTCACG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCATTTCACG
** * *
924870 TTGCGATTTTGGTTTCTCGTTGCGATTCTCATTTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCATTTCACG
* *
924908 TTGCGATTTTAAGTTTCGTGTTGCGA
1 TTGCGATTTTCA-TTTCGCGTTGCGA
924934 AAGTAAACTA
Statistics
Matches: 112, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
31 2 0.02
32 1 0.01
33 51 0.46
34 1 0.01
35 1 0.01
36 2 0.02
38 43 0.38
39 11 0.10
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (38 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCATTTCACG
Found at i:926879 original size:14 final size:14
Alignment explanation
Indices: 926860--926895 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
926850 ATTGTTTAAT
926860 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
926874 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
926888 TGATTTGT
1 TGATTTGT
926896 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:927018 original size:19 final size:19
Alignment explanation
Indices: 927002--927099 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
926992 AAAAATGACT
927002 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
927021 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
927040 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
927054 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
927073 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
927093 ATCGCAA
1 ATCGCAA
927100 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:927131 original size:53 final size:53
Alignment explanation
Indices: 927002--927118 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
926992 AAAAATGACT
927002 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
927054 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
927107 ATCGCAATGCGA
1 ATCGCAATGCGA
927119 TTTTAATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.45
53 35 0.55
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:927136 original size:19 final size:19
Alignment explanation
Indices: 927108--927330 Score: 207
Period size: 19 Copynumber: 12.7 Consensus size: 19
927098 AACGAGAGAA
* *
927108 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
927127 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
*
927143 TCG--TTGCGATTTTCATC
1 TCGCATTGCGATTTTCATT
927160 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
927179 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
*
927195 TCG--TTGCAATTTTCATT
1 TCGCATTGCGATTTTCATT
927212 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
927231 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
927248 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
927265 TCACATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
927284 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
927302 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
927318 TCGCATTGCGATT
1 TCGCATTGCGATT
927331 CTCTCGTTGC
Statistics
Matches: 168, Mismatches: 14, Indels: 44
0.74 0.06 0.19
Matches are distributed among these distances:
14 28 0.17
16 21 0.12
17 20 0.12
18 4 0.02
19 70 0.42
20 25 0.15
ACGTcount: A:0.16, C:0.22, G:0.17, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:927151 original size:33 final size:33
Alignment explanation
Indices: 927114--927277 Score: 138
Period size: 33 Copynumber: 4.8 Consensus size: 33
927104 AGAATCGCAA
*
927114 TGCGATTTTAATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
* *
927147 TGCGATTTTCATCTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
* * * *
927185 TGCGATTCTCTC-GTT-GCAATTTTC-ATT-TCGCAT
1 TGCGATT-T-TCATTTCGC-A-TTGCGATTCTCTCGT
927218 TGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
*
927252 TGCGATTTTCATTTCACATTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATT
927278 TTCATTTCCG
Statistics
Matches: 103, Mismatches: 14, Indels: 28
0.71 0.10 0.19
Matches are distributed among these distances:
31 2 0.02
32 6 0.06
33 45 0.44
34 20 0.19
35 5 0.05
36 4 0.04
37 2 0.02
38 10 0.10
39 4 0.04
40 5 0.05
ACGTcount: A:0.15, C:0.23, G:0.16, T:0.45
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:927260 original size:53 final size:52
Alignment explanation
Indices: 927108--927330 Score: 349
Period size: 53 Copynumber: 4.2 Consensus size: 52
927098 AACGAGAGAA
* * *
927108 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATC
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
927160 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCAATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
927212 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATTTTCATT
* * *
927265 TCACATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCATT
1 TCGCATTGCGATTTTCATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTCATT
927318 TCGCATTGCGATT
1 TCGCATTGCGATT
927331 CTCTCGTTGC
Statistics
Matches: 160, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
52 68 0.43
53 91 0.57
54 1 0.01
ACGTcount: A:0.16, C:0.22, G:0.17, T:0.45
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:927272 original size:86 final size:84
Alignment explanation
Indices: 927165--927344 Score: 224
Period size: 86 Copynumber: 2.1 Consensus size: 84
927155 TCATCTCGCA
*
927165 TTGCGATTTTCATTTCGCATTGCGA-TTC-TCT-CG-TTGCAATTTTCATTTCGCATTGCGATTT
1 TTGCGATTTTCATTTCACATTGCGATTTCATCTCCGATTGCAATTTTCA--T-G--TTGCGATTT
927226 TCATTTCCGCATTGCGATTCTCTCG
61 TCATTT-CGCATTGCGATTCTCTCG
* * *
927251 TTGCGATTTTCATTTCACATTGCGATTTTCATTTCCGCATTGCGATTTTCATGTTGGGATTTTCA
1 TTGCGATTTTCATTTCACATTGCGA-TTTCATCTCCG-ATTGCAATTTTCATGTTGCGATTTTCA
927316 TTTCGCATTGCGATTCTCTCG
64 TTTCGCATTGCGATTCTCTCG
927337 TTGCGATT
1 TTGCGATT
927345 GTAATTTCCG
Statistics
Matches: 84, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
86 50 0.60
87 14 0.17
88 3 0.04
89 3 0.04
90 3 0.04
92 11 0.13
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (84 bp):
TTGCGATTTTCATTTCACATTGCGATTTCATCTCCGATTGCAATTTTCATGTTGCGATTTTCATT
TCGCATTGCGATTCTCTCG
Found at i:927328 original size:33 final size:34
Alignment explanation
Indices: 927146--927344 Score: 167
Period size: 33 Copynumber: 5.7 Consensus size: 34
927136 GATTCTCTCG
927146 TTGCGATTTTCATCTCGCATTGCGATTTTCATTTCGCA
1 TTGCGATTTTCA--TCG--TTGCGATTTTCATTTCGCA
* *
927184 TTGCGATTCTC-TCGTTGCAATTTTCATTTCGCA
1 TTGCGATTTTCATCGTTGCGATTTTCATTTCGCA
* * * *
927217 TTGCGATTTTCAT--TTCCGCA-TTGCGATTCTCTCG
1 TTGCGATTTTCATCGTTGCG-ATTTTC-ATT-TCGCA
*
927251 TTGCGATTTTCATTTCACATTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCA--T--CGTTGCGATTTTCATTT-CGCA
*
927290 TTGCGATTTTCAT-GTTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATCGTTGCGATTTTCATTTCGCA
*
927323 TTGCGATTCTC-TCGTTGCGATT
1 TTGCGATTTTCATCGTTGCGATT
927345 GTAATTTCCG
Statistics
Matches: 132, Mismatches: 16, Indels: 31
0.74 0.09 0.17
Matches are distributed among these distances:
32 7 0.05
33 54 0.41
34 30 0.23
35 3 0.02
36 1 0.01
37 1 0.01
38 11 0.08
39 18 0.14
40 7 0.05
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.46
Consensus pattern (34 bp):
TTGCGATTTTCATCGTTGCGATTTTCATTTCGCA
Found at i:927359 original size:53 final size:53
Alignment explanation
Indices: 927145--927363 Score: 191
Period size: 53 Copynumber: 4.2 Consensus size: 53
927135 CGATTCTCTC
* * * *
927145 GTTGCGATTTTCATCTCGCATTGCGATTTTCA-TTTCGCATTGCGA-TTCTC-T
1 GTTGCGATTTTCATTTCACATTGCGATTTTCAGTTCCGCATTGCAATTTC-CAT
* * * *
927196 CGTTGCAATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGA-TTCTC-T
1 -GTTGCGATTTTCATTTCACATTGCGATTTTCAGTTCCGCATTGCAATTTC-CAT
* * *
927249 CGTTGCGATTTTCATTTCACATTGCGATTTTCATTTCCGCATTGCGATTTTCAT
1 -GTTGCGATTTTCATTTCACATTGCGATTTTCAGTTCCGCATTGCAATTTCCAT
* * * * *
927303 GTTGGGATTTTCATTTCGCATTGCGATTCTCTC-GTTGCG-ATTGTAATTTCCGT
1 GTTGCGATTTTCATTTCACATTGCGATT-T-TCAGTTCCGCATTGCAATTTCCAT
927356 GTTGCGAT
1 GTTGCGAT
927364 AGTCAAATGC
Statistics
Matches: 147, Mismatches: 15, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
52 30 0.20
53 107 0.73
54 8 0.05
55 2 0.01
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (53 bp):
GTTGCGATTTTCATTTCACATTGCGATTTTCAGTTCCGCATTGCAATTTCCAT
Found at i:929646 original size:12 final size:12
Alignment explanation
Indices: 929629--929653 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
929619 TCTTCGGGGA
929629 CTTTTTCTTCTT
1 CTTTTTCTTCTT
929641 CTTTTTCTTCTT
1 CTTTTTCTTCTT
929653 C
1 C
929654 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:929862 original size:24 final size:24
Alignment explanation
Indices: 929828--929874 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
929818 CTGAAACATC
929828 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
929852 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
929875 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:930595 original size:20 final size:20
Alignment explanation
Indices: 930567--930795 Score: 262
Period size: 20 Copynumber: 11.4 Consensus size: 20
930557 AAATTTCAGT
* * *
930567 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
930587 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
930607 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
*
930627 GTTGCGATTTACGGATTCTC
1 GTTGCGATTTACGGATTCGC
*
930647 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
930667 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
930687 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
930707 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
930727 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
930747 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
930767 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
930787 GTTGCGATT
1 GTTGCGATT
930796 CTGTAAAATC
Statistics
Matches: 187, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
20 186 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:930813 original size:21 final size:20
Alignment explanation
Indices: 930789--930838 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
930779 ATATTCGCGT
930789 TGCGATTCTGTAAAATCGCAA
1 TGCGATT-TGTAAAATCGCAA
** *
930810 TGCGAATTTGTACTATCGCAT
1 TGCG-ATTTGTAAAATCGCAA
930831 TGCGATTT
1 TGCGATTT
930839 TCAAGAATCG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 4 0.16
21 18 0.72
22 3 0.12
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (20 bp):
TGCGATTTGTAAAATCGCAA
Found at i:936719 original size:29 final size:29
Alignment explanation
Indices: 936677--936735 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
936667 ATTTTCACCT
936677 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
936706 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
936735 A
1 A
936736 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:941412 original size:29 final size:29
Alignment explanation
Indices: 941370--941455 Score: 163
Period size: 29 Copynumber: 3.0 Consensus size: 29
941360 TTTTCACCTA
941370 ACTAAATTGATGTAAGCAATGACATCAAG
1 ACTAAATTGATGTAAGCAATGACATCAAG
941399 ACTAAATTGATGTAAGCAATGACATCAAG
1 ACTAAATTGATGTAAGCAATGACATCAAG
*
941428 ACTAAATTGATGTAAACAATGACATCAA
1 ACTAAATTGATGTAAGCAATGACATCAA
941456 ATTAATTTAA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 56 1.00
ACGTcount: A:0.47, C:0.14, G:0.15, T:0.24
Consensus pattern (29 bp):
ACTAAATTGATGTAAGCAATGACATCAAG
Found at i:941651 original size:19 final size:19
Alignment explanation
Indices: 941627--941664 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
941617 ATATTTTTTA
941627 TTGAAAACTATAATTATTT
1 TTGAAAACTATAATTATTT
* *
941646 TTGAAATCTATAGTTATTT
1 TTGAAAACTATAATTATTT
941665 AATATTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (19 bp):
TTGAAAACTATAATTATTT
Found at i:942660 original size:23 final size:23
Alignment explanation
Indices: 942615--942663 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
942605 AAAGGTAGAA
*
942615 AAATATGCCACAAAGCCATAGAT
1 AAATATGCCACAAAGCCAGAGAT
942638 AAATATGCCACAAATG-CAGAGAT
1 AAATATGCCACAAA-GCCAGAGAT
942661 AAA
1 AAA
942664 CATGTTACTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 23 0.96
24 1 0.04
ACGTcount: A:0.51, C:0.18, G:0.14, T:0.16
Consensus pattern (23 bp):
AAATATGCCACAAAGCCAGAGAT
Found at i:946651 original size:19 final size:19
Alignment explanation
Indices: 946624--946661 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
946614 TCCAAAAACG
946624 TGTTATTTATTTGCAAATT
1 TGTTATTTATTTGCAAATT
*
946643 TGTTCTTTATTTGCAAATT
1 TGTTATTTATTTGCAAATT
946662 GACAAATGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.08, G:0.11, T:0.58
Consensus pattern (19 bp):
TGTTATTTATTTGCAAATT
Found at i:950885 original size:23 final size:23
Alignment explanation
Indices: 950859--950902 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
950849 ACGTATTAGA
950859 TACCGTTTATATAATATAATAGG
1 TACCGTTTATATAATATAATAGG
950882 TACCGTTTATATAATATAATA
1 TACCGTTTATATAATATAATA
950903 AGTTAATTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (23 bp):
TACCGTTTATATAATATAATAGG
Found at i:950966 original size:87 final size:86
Alignment explanation
Indices: 950843--951086 Score: 310
Period size: 87 Copynumber: 2.8 Consensus size: 86
950833 CGTTTAAAAA
* * * * *
950843 ACAATAACGTATTAGATACCGTTTATATAATATAATAGGTACCGTTTATATAATATAATAAGTTA
1 ACAATAACATATTAGGTA-CGTTTATATAATGTAATAGGTAACGTTTATATAATAAAATAAGTTA
*
950908 ATTA-CAGAAAATATTATCAAAC
65 ATTATCAG-AAACATTATCAAAC
* *
950930 ACAATAACATATTAGGTACAATTTATATAATGTAATAGATAACGTTTATATAATAAAATAAGTTA
1 ACAATAACATATTAGGTAC-GTTTATATAATGTAATAGGTAACGTTTATATAATAAAATAAGTTA
* *
950995 ATTATTAGAAACATTATTAAAC
65 ATTATCAGAAACATTATCAAAC
* * ** *
951017 ACAATAACATATTAGGTAGCGTTTATATAACGTAATATGTAGTGTTTATATAATAAAATATGTTA
1 ACAATAACATATTAGGTA-CGTTTATATAATGTAATAGGTAACGTTTATATAATAAAATAAGTTA
951082 ATTAT
65 ATTAT
951087 TTAATTTGTT
Statistics
Matches: 137, Mismatches: 17, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
86 1 0.01
87 133 0.97
88 3 0.02
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (86 bp):
ACAATAACATATTAGGTACGTTTATATAATGTAATAGGTAACGTTTATATAATAAAATAAGTTAA
TTATCAGAAACATTATCAAAC
Found at i:951046 original size:23 final size:23
Alignment explanation
Indices: 951020--951069 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
951010 ATTAAACACA
*
951020 ATAACATATTAGGTAGCGTTTAT
1 ATAACATAATAGGTAGCGTTTAT
* * *
951043 ATAACGTAATATGTAGTGTTTAT
1 ATAACATAATAGGTAGCGTTTAT
951066 ATAA
1 ATAA
951070 TAAAATATGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.06, G:0.16, T:0.40
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGTTTAT
Found at i:951076 original size:23 final size:23
Alignment explanation
Indices: 951032--951079 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
951022 AACATATTAG
**
951032 GTAGCGTTTATATAACGTAATAT
1 GTAGCGTTTATATAACAAAATAT
* *
951055 GTAGTGTTTATATAATAAAATAT
1 GTAGCGTTTATATAACAAAATAT
951078 GT
1 GT
951080 TAATTATTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.04, G:0.17, T:0.42
Consensus pattern (23 bp):
GTAGCGTTTATATAACAAAATAT
Found at i:951477 original size:23 final size:23
Alignment explanation
Indices: 951451--951517 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
951441 CTAGTAATTA
* *
951451 ACTTATTTTATTACATAAGCGCT
1 ACTTATTATATTATATAAGCGCT
* *
951474 ACTTATTACATTATATAAGCGTT
1 ACTTATTATATTATATAAGCGCT
*
951497 ACCTATTATATTATATAAGCG
1 ACTTATTATATTATATAAGCG
951518 GTATCTAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.42
Consensus pattern (23 bp):
ACTTATTATATTATATAAGCGCT
Found at i:951533 original size:23 final size:23
Alignment explanation
Indices: 951459--951533 Score: 69
Period size: 23 Copynumber: 3.3 Consensus size: 23
951449 TAACTTATTT
* * * *
951459 TATTACATAAGCGCTACTTATTA
1 TATTATATAAGCGGTACCTAATA
* * *
951482 CATTATATAAGCGTTACCTATTA
1 TATTATATAAGCGGTACCTAATA
*
951505 TATTATATAAGCGGTATCTAATA
1 TATTATATAAGCGGTACCTAATA
*
951528 TGTTAT
1 TATTAT
951534 TGTGCTTGAT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (23 bp):
TATTATATAAGCGGTACCTAATA
Found at i:952122 original size:2 final size:2
Alignment explanation
Indices: 952115--952158 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
952105 GTATGGACAC
952115 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
952157 AT
1 AT
952159 CGATACTTAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:954678 original size:37 final size:37
Alignment explanation
Indices: 954602--954678 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
954592 TTTTTATATT
*
954602 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
954639 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
954676 TTT
1 TTT
954679 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:958337 original size:17 final size:18
Alignment explanation
Indices: 958315--958356 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
958305 TTACACCTTT
*
958315 AAATAAATTTTTACAT-A
1 AAATAAATTTTTAAATGA
*
958332 AAATAATTTTTTAAATGA
1 AAATAAATTTTTAAATGA
958350 AAATAAA
1 AAATAAA
958357 ATTAAAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (18 bp):
AAATAAATTTTTAAATGA
Found at i:958389 original size:27 final size:27
Alignment explanation
Indices: 958359--958447 Score: 80
Period size: 25 Copynumber: 3.3 Consensus size: 27
958349 AAAATAAAAT
958359 TAAAATATTTTTAAATTAAGTTAATAA
1 TAAAATATTTTTAAATTAAGTTAATAA
* *
958386 TAAAATATTGTT-GA-TAAGTTAAT-A
1 TAAAATATTTTTAAATTAAGTTAATAA
*
958410 TAAAAATATTTTTTAAGTTAA--TATATATA
1 T-AAAATA-TTTTTAAATTAAGTTA-ATA-A
958439 TAAAATATT
1 TAAAATATT
958448 ATGAATTTAA
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
24 2 0.04
25 15 0.30
26 7 0.14
27 15 0.30
28 9 0.18
29 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (27 bp):
TAAAATATTTTTAAATTAAGTTAATAA
Found at i:958430 original size:23 final size:26
Alignment explanation
Indices: 958374--958436 Score: 89
Period size: 25 Copynumber: 2.6 Consensus size: 26
958364 TATTTTTAAA
958374 TTAAGTTAATA-ATAAAATATTGTTG
1 TTAAGTTAATATATAAAATATTGTTG
*
958399 ATAAGTTAATATA-AAAATATT-TT-
1 TTAAGTTAATATATAAAATATTGTTG
958422 TTAAGTTAATATATA
1 TTAAGTTAATATATA
958437 TATAAAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 12 0.35
24 3 0.09
25 18 0.53
26 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (26 bp):
TTAAGTTAATATATAAAATATTGTTG
Found at i:958991 original size:20 final size:21
Alignment explanation
Indices: 958963--959002 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
958953 TATAAGATTA
958963 TTTATTTTAGAGTTTAAAGAT
1 TTTATTTTAGAGTTTAAAGAT
*
958984 TTTA-TTTAGGGTTTAAAGA
1 TTTATTTTAGAGTTTAAAGA
959003 CTTAAGACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (21 bp):
TTTATTTTAGAGTTTAAAGAT
Found at i:959495 original size:19 final size:19
Alignment explanation
Indices: 959455--959495 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
959445 TAAAAAACAG
* * *
959455 TATAATATATATATATATA
1 TATAATATAAATACATAAA
959474 TATAATATAAATACATAAA
1 TATAATATAAATACATAAA
959493 TAT
1 TAT
959496 CTTTAGATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (19 bp):
TATAATATAAATACATAAA
Found at i:974732 original size:19 final size:19
Alignment explanation
Indices: 974704--974752 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
974694 GTAATCTGAG
974704 CAGAGATCAGA-ATAGAAAT
1 CAGAGATCAGAGA-AGAAAT
*
974723 CAGAGTTCAGAGAAGAAAT
1 CAGAGATCAGAGAAGAAAT
*
974742 CAGAGGTCAGA
1 CAGAGATCAGA
974753 TTGTATTCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 26 0.96
20 1 0.04
ACGTcount: A:0.47, C:0.12, G:0.27, T:0.14
Consensus pattern (19 bp):
CAGAGATCAGAGAAGAAAT
Found at i:975519 original size:25 final size:25
Alignment explanation
Indices: 975485--975541 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
975475 TTGTTCATTT
975485 CAGAGCTGAGGGTAATTAATTATTC
1 CAGAGCTGAGGGTAATTAATTATTC
975510 CAGAGCTGAGGGTAATTAATTATTC
1 CAGAGCTGAGGGTAATTAATTATTC
975535 CAGAGCT
1 CAGAGCT
975542 TGGACGTGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.30
Consensus pattern (25 bp):
CAGAGCTGAGGGTAATTAATTATTC
Found at i:980487 original size:3 final size:3
Alignment explanation
Indices: 980481--980562 Score: 51
Period size: 3 Copynumber: 27.7 Consensus size: 3
980471 TTCATTTGAA
* * *
980481 TAT TAT T-T ATAT TAT TTT TAT TTT TAT TAT TAT TAT TAT TAT AAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * *
980526 AAT AAT AAT AAT AAT AAT AAT TA- TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
980563 AATAATTTTA
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
2 3 0.04
3 66 0.94
4 1 0.01
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:981303 original size:26 final size:26
Alignment explanation
Indices: 981274--981324 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
981264 CCACCGGAGA
* *
981274 CGGTGGCCGGCGGCAGCGGGCGATGG
1 CGGTGGACGACGGCAGCGGGCGATGG
* *
981300 CGGTGTATGACGGCAGCGGGCGATG
1 CGGTGGACGACGGCAGCGGGCGATG
981325 ACGGCCGGTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.12, C:0.24, G:0.53, T:0.12
Consensus pattern (26 bp):
CGGTGGACGACGGCAGCGGGCGATGG
Found at i:981507 original size:14 final size:14
Alignment explanation
Indices: 981484--981513 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
981474 TCACCAAAAC
981484 GACGTAGTTTTGGT
1 GACGTAGTTTTGGT
*
981498 GACGTCGTTTTGGT
1 GACGTAGTTTTGGT
981512 GA
1 GA
981514 GGACTTCTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.13, C:0.10, G:0.37, T:0.40
Consensus pattern (14 bp):
GACGTAGTTTTGGT
Found at i:982516 original size:12 final size:12
Alignment explanation
Indices: 982473--982513 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
982463 ATTACTTTTA
982473 TATTTTAATTAT
1 TATTTTAATTAT
**
982485 TGCTTTAATTAT
1 TATTTTAATTAT
982497 TATTTT-ATTAT
1 TATTTTAATTAT
982508 TATTTT
1 TATTTT
982514 TATCTTATTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
11 11 0.44
12 14 0.56
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (12 bp):
TATTTTAATTAT
Found at i:982522 original size:14 final size:11
Alignment explanation
Indices: 982451--982513 Score: 51
Period size: 11 Copynumber: 5.8 Consensus size: 11
982441 TTATTTACAA
982451 TATTATTTTAT
1 TATTATTTTAT
*
982462 CATTACTTTTA-
1 TATTA-TTTTAT
*
982473 TA-T-TTTAAT
1 TATTATTTTAT
* *
982482 TATTGCTTTAAT
1 TATT-ATTTTAT
982494 TATTATTTTAT
1 TATTATTTTAT
982505 TATTATTTT
1 TATTATTTT
982514 TATCTTATTC
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
8 4 0.10
9 2 0.05
10 2 0.05
11 19 0.45
12 15 0.36
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.67
Consensus pattern (11 bp):
TATTATTTTAT
Found at i:992267 original size:42 final size:40
Alignment explanation
Indices: 992211--992292 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 40
992201 GATTATCAAA
992211 TTTTAATAAAAAAATAAAT-ATATAAATAATTATTTTATAAT
1 TTTTAATAAAAAAATAAATAATA-AAATAA-TATTTTATAAT
* **
992252 TTTTAATAATTAAAATATTTAATAAAATAATATTTTATAAT
1 TTTTAATAA-AAAAATAAATAATAAAATAATATTTTATAAT
992293 CCTGAATCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
41 20 0.56
42 13 0.36
43 3 0.08
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (40 bp):
TTTTAATAAAAAAATAAATAATAAAATAATATTTTATAAT
Found at i:992285 original size:15 final size:16
Alignment explanation
Indices: 992247--992292 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
992237 TAATTATTTT
*
992247 ATAATTTTTAATAATTA
1 ATAATATTTAATAA-TA
992264 A-AATATTTAATAA-A
1 ATAATATTTAATAATA
*
992278 ATAATATTTTATAAT
1 ATAATATTTAATAAT
992293 CCTGAATCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
14 2 0.08
15 11 0.44
16 11 0.44
17 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATAATATTTAATAATA
Found at i:993044 original size:2 final size:2
Alignment explanation
Indices: 993037--993106 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
993027 TGTTCATCCC
993037 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
993079 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
993107 AGTAAAATGT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:995827 original size:17 final size:17
Alignment explanation
Indices: 995791--995829 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
995781 ACATATTCAG
* *
995791 ATTTTAATCGAATATGA
1 ATTTAAATCGAATATAA
*
995808 ATTTAAATCGAATTTAA
1 ATTTAAATCGAATATAA
995825 ATTTA
1 ATTTA
995830 GATTCGAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.44
Consensus pattern (17 bp):
ATTTAAATCGAATATAA
Found at i:997995 original size:65 final size:66
Alignment explanation
Indices: 997850--997999 Score: 182
Period size: 65 Copynumber: 2.3 Consensus size: 66
997840 CCCTATTTCA
* * *
997850 AATGCAT-TTTGTGTACCGATGCATAGACCATGCATCAATGCACTCTTGAATTTATTGAAACATC
1 AATGCATATTAGTGTACCGATGCACAGACCATGCATCAATGCACTCCTGAATTTATTGAAACATC
997914 G
66 G
* * ** *
997915 AATGCATTTTA-TGTACCGATGCACAGACCATGCATCGATGCACTCCTGGCTCTT-TTGGAACAT
1 AATGCATATTAGTGTACCGATGCACAGACCATGCATCAATGCACTCCTGAAT-TTATTGAAACAT
997978 CG
65 CG
*
997980 AATGTA-ATTAGTGTACCGAT
1 AATGCATATTAGTGTACCGAT
998000 ACACCCCTAG
Statistics
Matches: 73, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
64 3 0.04
65 66 0.90
66 4 0.05
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (66 bp):
AATGCATATTAGTGTACCGATGCACAGACCATGCATCAATGCACTCCTGAATTTATTGAAACATC
G
Found at i:1001936 original size:41 final size:41
Alignment explanation
Indices: 1001879--1001976 Score: 178
Period size: 41 Copynumber: 2.4 Consensus size: 41
1001869 TAGTTCCTTA
* *
1001879 TCTAATTCAATGCATTTAATCCTATTGTTAAATGCAGCACG
1 TCTAATTCAATGCATTTAATCCTACTGTTAAATGCAACACG
1001920 TCTAATTCAATGCATTTAATCCTACTGTTAAATGCAACACG
1 TCTAATTCAATGCATTTAATCCTACTGTTAAATGCAACACG
1001961 TCTAATTCAATGCATT
1 TCTAATTCAATGCATT
1001977 ATCTTGCTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (41 bp):
TCTAATTCAATGCATTTAATCCTACTGTTAAATGCAACACG
Found at i:1009422 original size:44 final size:44
Alignment explanation
Indices: 1009361--1009466 Score: 128
Period size: 44 Copynumber: 2.5 Consensus size: 44
1009351 TAATATTTTC
*
1009361 AAATAATATA-ATTTATAATTA-TTTGTTATATTTTAAACAATT
1 AAATAATATATTTTTATAATTATTTTGTTATATTTTAAACAATT
* * *
1009403 AAATTAATATATTTTTATAA-TATTTTTTTATATTTTTAATAATT
1 AAA-TAATATATTTTTATAATTATTTTGTTATATTTTAAACAATT
* *
1009447 TAATAATATATTTTCATAAT
1 AAATAATATATTTTTATAAT
1009467 GCAAAAATAA
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
42 3 0.06
43 24 0.44
44 27 0.50
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (44 bp):
AAATAATATATTTTTATAATTATTTTGTTATATTTTAAACAATT
Found at i:1009447 original size:10 final size:11
Alignment explanation
Indices: 1009406--1009460 Score: 53
Period size: 11 Copynumber: 5.1 Consensus size: 11
1009396 AACAATTAAA
1009406 TTAATATATTT
1 TTAATATATTT
1009417 TT-ATAATATTT
1 TTAAT-ATATTT
*
1009428 TT-TTATATTT
1 TTAATATATTT
1009438 TTAATA-ATTT
1 TTAATATATTT
*
1009448 AATAATATATTT
1 -TTAATATATTT
1009460 T
1 T
1009461 CATAATGCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
10 14 0.39
11 18 0.50
12 4 0.11
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TTAATATATTT
Found at i:1009460 original size:21 final size:21
Alignment explanation
Indices: 1009387--1009466 Score: 54
Period size: 22 Copynumber: 3.7 Consensus size: 21
1009377 AATTATTTGT
* *
1009387 TATATTTTAAACAATTAAATTAA
1 TATATTTT-AATAATTTAA-TAA
* * **
1009410 TATATTTTTATAATATT-TTTT
1 TATATTTTAATAAT-TTAATAA
1009431 TATATTTTTAATAATTTAATAA
1 TATA-TTTTAATAATTTAATAA
*
1009453 TATATTTTCATAAT
1 TATATTTTAATAAT
1009467 GCAAAAATAA
Statistics
Matches: 43, Mismatches: 11, Indels: 8
0.69 0.18 0.13
Matches are distributed among these distances:
21 16 0.37
22 18 0.42
23 9 0.21
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (21 bp):
TATATTTTAATAATTTAATAA
Found at i:1009522 original size:18 final size:18
Alignment explanation
Indices: 1009483--1009523 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1009473 ATAAAAATTT
*
1009483 TAAA-ATATAAAATATAA
1 TAAATATATAAAAAATAA
1009500 TAAATATATACAAAAATAA
1 TAAATATATA-AAAAATAA
1009519 -AAATA
1 TAAATA
1009524 ATCGAGTCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 4 0.19
18 10 0.48
19 7 0.33
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (18 bp):
TAAATATATAAAAAATAA
Found at i:1010789 original size:16 final size:15
Alignment explanation
Indices: 1010770--1010799 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1010760 GATGAAAATG
1010770 ATATTATTGTAAAAAA
1 ATATTATT-TAAAAAA
1010786 ATATTATTTAAAAA
1 ATATTATTTAAAAA
1010800 TATCTAACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (15 bp):
ATATTATTTAAAAAA
Found at i:1011974 original size:2 final size:2
Alignment explanation
Indices: 1011967--1011996 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1011957 GATAATTTTA
1011967 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1011997 TAGTTTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1012232 original size:2 final size:2
Alignment explanation
Indices: 1012227--1012302 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
1012217 ACACACACAC
1012227 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1012269 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1012303 CCTTAAAATA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1013411 original size:18 final size:15
Alignment explanation
Indices: 1013388--1013427 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
1013378 CACAATTTGC
1013388 CAACTTGCCAACTTGAAT
1 CAACTTG-CAACTTG--T
1013406 CAACTTGCAACTTGT
1 CAACTTGCAACTTGT
1013421 CAACTTG
1 CAACTTG
1013428 TGGTAGTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.36
17 7 0.32
18 7 0.32
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.30
Consensus pattern (15 bp):
CAACTTGCAACTTGT
Found at i:1018193 original size:17 final size:18
Alignment explanation
Indices: 1018163--1018204 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
1018153 CACAATTTGA
1018163 CAACTTGCCAACTTGAAT
1 CAACTTGCCAACTTGAAT
*
1018181 CAACTTG-CAACTTGTAT
1 CAACTTGCCAACTTGAAT
1018198 CAACTTG
1 CAACTTG
1018205 TGGTAGTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.31
Consensus pattern (18 bp):
CAACTTGCCAACTTGAAT
Found at i:1026933 original size:36 final size:36
Alignment explanation
Indices: 1026886--1026964 Score: 149
Period size: 36 Copynumber: 2.2 Consensus size: 36
1026876 TACAATTCTT
1026886 AAAACTGTACATTATGATATCAATTAGAATATTAGG
1 AAAACTGTACATTATGATATCAATTAGAATATTAGG
*
1026922 AAAACTGTACATTATGATGTCAATTAGAATATTAGG
1 AAAACTGTACATTATGATATCAATTAGAATATTAGG
1026958 AAAACTG
1 AAAACTG
1026965 AAAGCATGAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.32
Consensus pattern (36 bp):
AAAACTGTACATTATGATATCAATTAGAATATTAGG
Found at i:1028290 original size:31 final size:31
Alignment explanation
Indices: 1028255--1028318 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 31
1028245 TTTTTAACGG
1028255 ATTAAAATT-TCAAGTTTAAATATTAAA-ACAA
1 ATTAAAATTAT-AA-TTTAAATATTAAACACAA
1028286 ATTAAAATTAATAATTTAAATATTAAACACAA
1 ATTAAAATT-ATAATTTAAATATTAAACACAA
1028318 A
1 A
1028319 ATTTACTCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
31 22 0.73
32 7 0.23
33 1 0.03
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.34
Consensus pattern (31 bp):
ATTAAAATTATAATTTAAATATTAAACACAA
Found at i:1028854 original size:17 final size:18
Alignment explanation
Indices: 1028834--1028874 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
1028824 ATCAATTCTT
1028834 AAAAAAAAT-AATAAACG
1 AAAAAAAATGAATAAACG
* *
1028851 -AAAATAATGACTAAACG
1 AAAAAAAATGAATAAACG
1028868 AAAAAAA
1 AAAAAAA
1028875 GTGTCAATAG
Statistics
Matches: 19, Mismatches: 3, Indels: 3
0.76 0.12 0.12
Matches are distributed among these distances:
16 7 0.37
17 7 0.37
18 5 0.26
ACGTcount: A:0.73, C:0.07, G:0.07, T:0.12
Consensus pattern (18 bp):
AAAAAAAATGAATAAACG
Found at i:1028917 original size:19 final size:19
Alignment explanation
Indices: 1028893--1028938 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
1028883 AGATAGAGGA
*
1028893 AAAAATGTCATAAAGACAC
1 AAAAATGTCATAAAAACAC
* *
1028912 AAAAATATCATAAAAACAG
1 AAAAATGTCATAAAAACAC
1028931 AAAAATGT
1 AAAAATGT
1028939 ATTATAAAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.63, C:0.11, G:0.09, T:0.17
Consensus pattern (19 bp):
AAAAATGTCATAAAAACAC
Found at i:1029365 original size:19 final size:18
Alignment explanation
Indices: 1029345--1029387 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
1029335 AGTAAAGTGT
1029345 TTTTAAAAAAAAAATAAG
1 TTTTAAAAAAAAAATAAG
* *
1029363 -TTTAATACAAAAATAAG
1 TTTTAAAAAAAAAATAAG
1029380 TGTTTAAA
1 T-TTTAAA
1029388 TTATATAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
17 15 0.75
19 5 0.25
ACGTcount: A:0.58, C:0.02, G:0.07, T:0.33
Consensus pattern (18 bp):
TTTTAAAAAAAAAATAAG
Found at i:1030450 original size:24 final size:23
Alignment explanation
Indices: 1030410--1030467 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 23
1030400 GTATTTATAT
* *
1030410 TAAAA-AAATATATATACACATA
1 TAAAATAAATAAAAATACACATA
* **
1030432 TATAATAGAATAAAAATACGTATA
1 TAAAATA-AATAAAAATACACATA
1030456 TAAAATAAATAA
1 TAAAATAAATAA
1030468 TATAAAATAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
22 4 0.14
23 6 0.21
24 18 0.64
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (23 bp):
TAAAATAAATAAAAATACACATA
Found at i:1031509 original size:2 final size:2
Alignment explanation
Indices: 1031502--1031553 Score: 79
Period size: 2 Copynumber: 26.5 Consensus size: 2
1031492 AAATGAAATA
* *
1031502 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1031544 AT AT AT -T AT A
1 AT AT AT AT AT A
1031554 ATAGCAATGG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1032310 original size:105 final size:105
Alignment explanation
Indices: 1031938--1032774 Score: 1177
Period size: 105 Copynumber: 8.0 Consensus size: 105
1031928 ATTATTCCGC
* * * * **
1031938 GTCCAATATCCTCCGCTGTGAAGTTGAAATTGGTTCTGGAATTGGGAAATTGTTTGTTGACAGTC
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TTGTTGACAACC
*** * * * **
1032003 AGCCACCCCTTCG-CTGTGAAGTTGAGCTTGTGCTGTCTCAA
65 AGCGGTCCCTTCGTC-GTGAAGTTGAACTTGCGTTGTCTGGA
* * **
1032044 GTCTAATATCCTTTGCTGTGAAGTTGAAA-TGGACTCTG-AA-T--GAAACT-TTGTTGACAACC
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGG-CTCTGAAATTGGGAAGTTGTTGTTGACAACC
* ** *
1032103 ATCGGTCATTTCGTCGTGAAGTTGAACTTGCGTTTTCTGGA
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
* *
1032144 GT-CAATATCCTTCGCTGGGAAGTTGAAATTAGCTCTGAAATTGGGAAGTTGTTGTTGACAACCA
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAACCA
* *
1032208 GCGGTCCCTTCGTCGTGAAGTTGAACTTGAGTCGTCTGGA
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
* * * *
1032248 GTCCAATATCCTTCCCTGTGAAGATGAAATTGGCTCTAAAATTGGGAAGTTGTTGTTGACAACTA
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAACCA
*
1032313 GCGGTCCCTTCGTCGTGAAGTTAAACTTGCGTTGTCTGGA
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
* *
1032353 GTTCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTGTTGTTGACAACCA
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAACCA
* *
1032418 GCGGTCCTTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGA
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
*
1032458 GTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAACCA
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAACCA
*
1032523 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTATGGA
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
*
1032563 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAGTTGTTGTTGACAACCA
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAACCA
* *
1032628 GCGGTCCCTTCATCGTGAAGTTGAACTTGCGTCGTCTGGA
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
* * *
1032668 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGAAAATTGTTGTTGACAACCA
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAACCA
* * *
1032733 GCCGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTTGA
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
1032773 GT
1 GT
1032775 GGCGCGATAT
Statistics
Matches: 657, Mismatches: 65, Indels: 19
0.89 0.09 0.03
Matches are distributed among these distances:
99 28 0.04
100 43 0.07
101 2 0.00
102 5 0.01
103 4 0.01
104 50 0.08
105 495 0.75
106 30 0.05
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.33
Consensus pattern (105 bp):
GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAACCA
GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
Found at i:1044454 original size:52 final size:50
Alignment explanation
Indices: 1044351--1044461 Score: 120
Period size: 50 Copynumber: 2.2 Consensus size: 50
1044341 ACTATAATTC
* * * * *
1044351 AATATATATATATATATATATAATAATGATCAATATAGTATTTATATTAA
1 AATATATATATATACACATATAATAATGATCAATATAGTATATAAAATAA
1044401 AATATATATATATACACATAT-ATAATAGAATACAA-ATACGTATATAAAATAA
1 AATATATATATATACACATATAATAAT-G-AT-CAATATA-GTATATAAAATAA
1044453 AATA-ATATA
1 AATATATATA
1044462 AAATAATAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
49 5 0.10
50 20 0.38
51 10 0.19
52 17 0.33
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.37
Consensus pattern (50 bp):
AATATATATATATACACATATAATAATGATCAATATAGTATATAAAATAA
Found at i:1044462 original size:15 final size:16
Alignment explanation
Indices: 1044442--1044475 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
1044432 ACAAATACGT
1044442 ATATAAAATAA-AATA
1 ATATAAAATAATAATA
1044457 ATATAAAATAATAATA
1 ATATAAAATAATAATA
1044473 ATA
1 ATA
1044476 ATAATAAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
ATATAAAATAATAATA
Found at i:1044469 original size:3 final size:3
Alignment explanation
Indices: 1044444--1044482 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
1044434 AAATACGTAT
1044444 ATA A-A ATA A-A ATA AT- ATA A-A ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1044483 AGGGATCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
2 8 0.25
3 24 0.75
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:1044474 original size:6 final size:6
Alignment explanation
Indices: 1044444--1044482 Score: 50
Period size: 5 Copynumber: 7.2 Consensus size: 6
1044434 AAATACGTAT
1044444 ATAA-A ATAA-A ATAAT- ATAA-A ATAATA ATAATA ATAATA A
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA A
1044483 AGGGATCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
5 17 0.55
6 14 0.45
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (6 bp):
ATAATA
Found at i:1045484 original size:2 final size:2
Alignment explanation
Indices: 1045477--1045508 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1045467 AAATGAAATA
1045477 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1045509 ATAGCAATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1046849 original size:6 final size:6
Alignment explanation
Indices: 1046838--1046904 Score: 107
Period size: 6 Copynumber: 11.2 Consensus size: 6
1046828 GACACGTATT
* * *
1046838 ACCACG ACCACG ACCACG ACCACG ACCACG ACCTCG ACCTCG ACCTCG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1046886 ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG A
1046905 GCCGAGCCGA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 59 1.00
ACGTcount: A:0.30, C:0.49, G:0.16, T:0.04
Consensus pattern (6 bp):
ACCACG
Found at i:1046912 original size:5 final size:5
Alignment explanation
Indices: 1046902--1046950 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
1046892 ACCACGACCA
* * * *
1046902 CGAGC CGAGC CGAGC CGAGC CGTGC CGTGC CGTGC CGAGC CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
1046951 ACGGACGGAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.16, C:0.37, G:0.41, T:0.06
Consensus pattern (5 bp):
CGAGC
Found at i:1052814 original size:6 final size:6
Alignment explanation
Indices: 1052803--1052881 Score: 122
Period size: 6 Copynumber: 13.2 Consensus size: 6
1052793 GACACGTATT
* *
1052803 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCTCG ACCTCG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
* *
1052851 ACCTCG ACCTCG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
1052882 GCCGAGCCGA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 71 1.00
ACGTcount: A:0.29, C:0.49, G:0.16, T:0.05
Consensus pattern (6 bp):
ACCACG
Found at i:1052889 original size:5 final size:5
Alignment explanation
Indices: 1052879--1052937 Score: 64
Period size: 5 Copynumber: 11.8 Consensus size: 5
1052869 ACCACGACCA
* * * * *
1052879 CGAGC CGAGC CGAGC CGAGC CGTGC CGTGC CGTGC CGTGC CGTGC CGAGC
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC
*
1052929 CGAGA CGAG
1 CGAGC CGAG
1052938 ACGGACGGAC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 51 1.00
ACGTcount: A:0.14, C:0.37, G:0.41, T:0.08
Consensus pattern (5 bp):
CGAGC
Found at i:1054231 original size:36 final size:36
Alignment explanation
Indices: 1054184--1054254 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
1054174 TTTGTTCCAA
*
1054184 AAACGCCGCAATAGGTTCTGATATTTAGCGACGTTC
1 AAACGCCGCAATAGGTTCTGACATTTAGCGACGTTC
* *
1054220 AAACGCCGCAATAGGTTTTGACATTTAGCGGCGTT
1 AAACGCCGCAATAGGTTCTGACATTTAGCGACGTT
1054255 TTTCTTAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (36 bp):
AAACGCCGCAATAGGTTCTGACATTTAGCGACGTTC
Found at i:1054459 original size:43 final size:44
Alignment explanation
Indices: 1054296--1054472 Score: 171
Period size: 44 Copynumber: 4.1 Consensus size: 44
1054286 TTTAGCGGTG
* * * * * *
1054296 TTTTTAGGATAAAAACGCAGATAAAAATTTTGTATATAACGG-A
1 TTTTTAGGATACAAACGCCGATAAAGATCTGGTATATAGCGGCA
* *
1054339 GTTTTTAGGATAAAAACGCAGATAAAGATCTGGTATATAGCGGC-
1 -TTTTTAGGATACAAACGCCGATAAAGATCTGGTATATAGCGGCA
* * *** *
1054383 GTTTTAGGATACAAACGCCGTTGTTGATCTGGTATATAGTGGCA
1 TTTTTAGGATACAAACGCCGATAAAGATCTGGTATATAGCGGCA
* * *
1054427 TTTTTAGTATACAAACGCCGCTAAAGGT-TGGTATATAGCGGCA
1 TTTTTAGGATACAAACGCCGATAAAGATCTGGTATATAGCGGCA
1054470 TTT
1 TTT
1054473 GTAACAAAAA
Statistics
Matches: 111, Mismatches: 20, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
43 52 0.47
44 59 0.53
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.32
Consensus pattern (44 bp):
TTTTTAGGATACAAACGCCGATAAAGATCTGGTATATAGCGGCA
Found at i:1058888 original size:14 final size:14
Alignment explanation
Indices: 1058869--1058896 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1058859 AAAAAGGACA
1058869 AGCATAACGACCTT
1 AGCATAACGACCTT
1058883 AGCATAACGACCTT
1 AGCATAACGACCTT
1058897 TGGTACTCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.14, T:0.21
Consensus pattern (14 bp):
AGCATAACGACCTT
Found at i:1063158 original size:41 final size:41
Alignment explanation
Indices: 1063072--1063165 Score: 107
Period size: 41 Copynumber: 2.3 Consensus size: 41
1063062 ATTTTTTTAC
* * * * * * *
1063072 AAACGCCACTAAATTATAGGGATATTGCGGCGTTCGGTCAC
1 AAACGCCACTAAAGTAGAAGGATATTACGGCGTTCGCTAAA
**
1063113 AAACGCCACTAAAGTAGAAGGATATTACGGCGTTTTCTAAA
1 AAACGCCACTAAAGTAGAAGGATATTACGGCGTTCGCTAAA
1063154 AAACGCCACTAA
1 AAACGCCACTAA
1063166 CGTTTATTGC
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.22
Consensus pattern (41 bp):
AAACGCCACTAAAGTAGAAGGATATTACGGCGTTCGCTAAA
Found at i:1063504 original size:18 final size:18
Alignment explanation
Indices: 1063483--1063521 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1063473 CAAATGTTTA
*
1063483 ATAAAAATACTAATCTAC
1 ATAAAAATACTAAACTAC
* *
1063501 ATAATAATCCTAAACTAC
1 ATAAAAATACTAAACTAC
1063519 ATA
1 ATA
1063522 CACTAAATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.18, G:0.00, T:0.28
Consensus pattern (18 bp):
ATAAAAATACTAAACTAC
Found at i:1064451 original size:22 final size:22
Alignment explanation
Indices: 1064426--1064470 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1064416 TTCAGAAGGT
*
1064426 ATTATTTTCCTATTAGAAAGCA
1 ATTATTTTACTATTAGAAAGCA
* *
1064448 ATTATTTTACTATTCGAATGCA
1 ATTATTTTACTATTAGAAAGCA
1064470 A
1 A
1064471 AAAAACACTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (22 bp):
ATTATTTTACTATTAGAAAGCA
Found at i:1068519 original size:23 final size:23
Alignment explanation
Indices: 1068489--1068549 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
1068479 GTAAAGGAAG
1068489 AGGAAGAAGATGAAGAGAAGCAA
1 AGGAAGAAGATGAAGAGAAGCAA
*
1068512 AGGAAGAAGATGAAGAGAATCAA
1 AGGAAGAAGATGAAGAGAAGCAA
** *
1068535 AACAAGAAGAAGAAG
1 AGGAAGAAGATGAAG
1068550 GAGGTAGGCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.59, C:0.05, G:0.31, T:0.05
Consensus pattern (23 bp):
AGGAAGAAGATGAAGAGAAGCAA
Found at i:1069069 original size:19 final size:19
Alignment explanation
Indices: 1069033--1069069 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1069023 TGAAAATGAT
*
1069033 TTGATTTTGAAAGCCAAAG
1 TTGATTTTGAAAACCAAAG
*
1069052 TTGATTTTGAAAATCAAA
1 TTGATTTTGAAAACCAAA
1069070 ATGAAATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (19 bp):
TTGATTTTGAAAACCAAAG
Found at i:1073906 original size:19 final size:20
Alignment explanation
Indices: 1073868--1073906 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1073858 AAGTGTTTAA
*
1073868 ATGATTTTTTAAATATTAATT
1 ATGATTTTTT-AATAATAATT
1073889 ATGATTTTTT-ATAATAAT
1 ATGATTTTTTAATAATAAT
1073907 AAAATGTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
21 10 0.59
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
ATGATTTTTTAATAATAATT
Done.