Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005221.1 Hibiscus syriacus cultivar Beakdansim tig00011821_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: 84185
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:8262 original size:60 final size:59
Alignment explanation
Indices: 8165--8297 Score: 169
Period size: 60 Copynumber: 2.2 Consensus size: 59
8155 TATATAGGGT
* *
8165 AAAGTATACAAATGGTACTCCGACTATAGAATGTTGCTTTGTTGAGTCC-TTCAACTATCA
1 AAAGT-TAAAAATGGTACTCCGACTATAGAATATTGCTTTGTTGAGTCCATT-AACTATCA
* * * *
8225 AAAGTTAAAAATGGATCCTCCGACTATAGGATATTGCTTTGTTGAGTCCATTGACTATTA
1 AAAGTTAAAAATGG-TACTCCGACTATAGAATATTGCTTTGTTGAGTCCATTAACTATCA
8285 AAAGTTACAAAAT
1 AAAGTTA-AAAAT
8298 AGTTATCTGA
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
59 8 0.12
60 49 0.77
61 7 0.11
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33
Consensus pattern (59 bp):
AAAGTTAAAAATGGTACTCCGACTATAGAATATTGCTTTGTTGAGTCCATTAACTATCA
Found at i:8644 original size:59 final size:59
Alignment explanation
Indices: 8520--8633 Score: 169
Period size: 59 Copynumber: 1.9 Consensus size: 59
8510 CAGATGATCA
8520 ATTTGTAACTTTTAATAGTCGAGAAACTCAACAAAGCAACAACCTATAGTCGATAGACC
1 ATTTGTAACTTTTAATAGTCGAGAAACTCAACAAAGCAACAACCTATAGTCGATAGACC
** * *
8579 ATTTGTAACTTTTGAA-AGTCGAGGGACTCAACAAAGCAATACCCTATAGTC-ATAG
1 ATTTGTAACTTTT-AATAGTCGAGAAACTCAACAAAGCAACAACCTATAGTCGATAG
8634 GGCTATTTGT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
58 4 0.08
59 44 0.88
60 2 0.04
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (59 bp):
ATTTGTAACTTTTAATAGTCGAGAAACTCAACAAAGCAACAACCTATAGTCGATAGACC
Found at i:14579 original size:42 final size:41
Alignment explanation
Indices: 14514--14931 Score: 188
Period size: 43 Copynumber: 9.8 Consensus size: 41
14504 TATAAAATTG
* * *
14514 TAAAAAAATTAGAGGCCTTAATTATAAAGGTAGAAATCGATAT
1 TAAAAAAATAAG-GGCCTCAATTATAAAGGTAGAAAT-GAGAT
* *
14557 TAAAAAAATAAGGGCCTCAATTATAAAGGTATAATTGAGAT
1 TAAAAAAATAAGGGCCTCAATTATAAAGGTAGAAATGAGAT
* * * * * *
14598 CGAAAAAACTTAGGGGCCTCAATTAGAAAGTTAGAAGTGAGAT
1 -TAAAAAA-ATAAGGGCCTCAATTATAAAGGTAGAAATGAGAT
* * * *
14641 TAAAAAAACTTAAGGGCCTAAATAAT-AAGGTTAAAAAAGTGGGAT
1 TAAAAAAA--TAAGGGCCTCAATTATAAAGG-T-AGAAA-TGAGAT
* * *
14686 T-AAAAAA-AGGGGCCTCAATTATAAAAGTGGAAATTGAGAT
1 TAAAAAAATAAGGGCCTCAATTATAAAGGTAGAAA-TGAGAT
* *
14726 TGAAAAAAAACTTAGGGGCCTCAATTGA-AAAGGTGGAAAGTGAGAT
1 T--AAAAAAA--TAAGGGCCTCAATT-ATAAAGGTAGAAA-TGAGAT
* * * * *
14772 TAAAAAAAACTTAAGGGTCTAAATAAT-AAGGTTAAAAAGTGGGAT
1 T-AAAAAAA--TAAGGGCCTCAATTATAAAGG-TAGAAA-TGAGAT
* * * *
14817 T-AAAAAA-AGGGGTCTCAATTATAAAAGTGGAAATTGAGAT
1 TAAAAAAATAAGGGCCTCAATTATAAAGGTAGAAA-TGAGAT
** * ** *
14857 TGAAAAAAACTTAAAAGCATCAATTATAAAATTA-AAAGTAAGAT
1 T-AAAAAAA--TAAGGGCCTCAATTATAAAGGTAGAAA-TGAGAT
* * *
14901 T-ACAAAATTAGGAGTCTCAATTATAAAGGTA
1 TAAAAAAATAAGG-GCCTCAATTATAAAGGTA
14932 AAAAAAGGGA
Statistics
Matches: 287, Mismatches: 64, Indels: 50
0.72 0.16 0.12
Matches are distributed among these distances:
40 33 0.11
41 34 0.12
42 50 0.17
43 64 0.22
44 23 0.08
45 52 0.18
46 30 0.10
47 1 0.00
ACGTcount: A:0.49, C:0.07, G:0.20, T:0.24
Consensus pattern (41 bp):
TAAAAAAATAAGGGCCTCAATTATAAAGGTAGAAATGAGAT
Found at i:14779 original size:45 final size:44
Alignment explanation
Indices: 14514--14869 Score: 210
Period size: 43 Copynumber: 8.3 Consensus size: 44
14504 TATAAAATTG
* * * *
14514 TAAAAAAA-TTAGAGGCCTTAATTATAAAGGTAGAAA-TCGATAT
1 TAAAAAAACTTAGGGGCCTCAATTAGAAAGGTAGAAAGT-GAGAT
* * * *
14557 TAAAAAAA--TAAGGGCCTCAATTATAAAGGTA-TAATTGAGAT
1 TAAAAAAACTTAGGGGCCTCAATTAGAAAGGTAGAAAGTGAGAT
** *
14598 CGAAAAAACTTAGGGGCCTCAATTAGAAAGTTAG-AAGTGAGAT
1 TAAAAAAACTTAGGGGCCTCAATTAGAAAGGTAGAAAGTGAGAT
* * * *
14641 TAAAAAAACTTAAGGGCCT-AAATA-ATAAGGTTAAAAAAGTGGGAT
1 TAAAAAAACTTAGGGGCCTCAATTAGA-AAGG-T-AGAAAGTGAGAT
* * * *
14686 T-AAAAAA---AGGGGCCTCAATTATAAAAGTGGAAATTGAGAT
1 TAAAAAAACTTAGGGGCCTCAATTAGAAAGGTAGAAAGTGAGAT
*
14726 TGAAAAAAAACTTAGGGGCCTCAATT-GAAAAGGTGGAAAGTGAGAT
1 T--AAAAAAACTTAGGGGCCTCAATTAG-AAAGGTAGAAAGTGAGAT
* * * * *
14772 TAAAAAAAACTTAAGGGTCT-AAATA-ATAAGGTTAAAAAGTGGGAT
1 T-AAAAAAACTTAGGGGCCTCAATTAGA-AAGG-TAGAAAGTGAGAT
* * * * *
14817 T-AAAAAA---AGGGGTCTCAATTATAAAAGTGGAAATTGAGAT
1 TAAAAAAACTTAGGGGCCTCAATTAGAAAGGTAGAAAGTGAGAT
14857 TGAAAAAAACTTA
1 T-AAAAAAACTTA
14870 AAAGCATCAA
Statistics
Matches: 245, Mismatches: 41, Indels: 52
0.72 0.12 0.15
Matches are distributed among these distances:
40 26 0.11
41 28 0.11
42 42 0.17
43 67 0.27
44 14 0.06
45 38 0.16
46 30 0.12
ACGTcount: A:0.48, C:0.07, G:0.21, T:0.24
Consensus pattern (44 bp):
TAAAAAAACTTAGGGGCCTCAATTAGAAAGGTAGAAAGTGAGAT
Found at i:14812 original size:131 final size:129
Alignment explanation
Indices: 14559--14869 Score: 470
Period size: 131 Copynumber: 2.4 Consensus size: 129
14549 ATCGATATTA
* * *
14559 AAAAAATAAGGGCCTCAATTAT-AAAG-GTATAATTGAGATCG-AAAAAACTTAGGGGCCTCAAT
1 AAAAAA-AGGGGCCTCAATTATAAAAGTGGA-AATTGAGATTGAAAAAAACTTAGGGGCCTCAAT
*
14621 TAGAAAGTTAGAAGTGAGATTAAAAAAACTTAAGGGCCTAAATAATAAGGTTAAAAAAGTGGGAT
64 TAGAAAGGTAGAAGTGAGATTAAAAAAACTTAAGGGCCTAAATAATAAGGTTAAAAAAGTGGGAT
14686 T
129 T
14687 AAAAAAAGGGGCCTCAATTATAAAAGTGGAAATTGAGATTGAAAAAAAACTTAGGGGCCTCAATT
1 AAAAAAAGGGGCCTCAATTATAAAAGTGGAAATTGAGATTG-AAAAAAACTTAGGGGCCTCAATT
* *
14752 -GAAAAGGTGGAAAGTGAGATTAAAAAAAACTTAAGGGTCTAAATAATAAGGTT-AAAAAGTGGG
65 AG-AAAGGTAG-AAGTGAGATT-AAAAAAACTTAAGGGCCTAAATAATAAGGTTAAAAAAGTGGG
14815 ATT
127 ATT
*
14818 AAAAAAAGGGGTCTCAATTATAAAAGTGGAAATTGAGATTGAAAAAAACTTA
1 AAAAAAAGGGGCCTCAATTATAAAAGTGGAAATTGAGATTGAAAAAAACTTA
14870 AAAGCATCAA
Statistics
Matches: 169, Mismatches: 7, Indels: 12
0.90 0.04 0.06
Matches are distributed among these distances:
127 14 0.08
128 20 0.12
129 3 0.02
130 39 0.23
131 63 0.37
132 30 0.18
ACGTcount: A:0.48, C:0.07, G:0.22, T:0.23
Consensus pattern (129 bp):
AAAAAAAGGGGCCTCAATTATAAAAGTGGAAATTGAGATTGAAAAAAACTTAGGGGCCTCAATTA
GAAAGGTAGAAGTGAGATTAAAAAAACTTAAGGGCCTAAATAATAAGGTTAAAAAAGTGGGATT
Found at i:14892 original size:85 final size:86
Alignment explanation
Indices: 14739--14927 Score: 197
Period size: 85 Copynumber: 2.2 Consensus size: 86
14729 AAAAAAACTT
* * ** **
14739 AGGGGCCTCAATTGA-AAAGGTGGAAAGTGAGATTAAAAAAAACTTAAGGGTCTAAATAATAAGG
1 AGGGGTCTCAATT-ATAAAAGTGGAAAGTGAGATTAAAAAAAACTTAAAAGTCTAAATAATAAAA
**
14803 TTAAAAAGTGGGATTA-AAAA-A
65 TT-AAAAGTAAGATTACAAAATA
* * * *
14824 AGGGGTCTCAATTATAAAAGTGGAAATTGAGATTGAAAAAAACTTAAAAG-CATCAATTATAAAA
1 AGGGGTCTCAATTATAAAAGTGGAAAGTGAGATTAAAAAAAACTTAAAAGTC-TAAATAATAAAA
*
14888 TTAAAAGTAAGATTACAAAATT
65 TTAAAAGTAAGATTACAAAATA
*
14910 AGGAGTCTCAATTATAAA
1 AGGGGTCTCAATTATAAA
14928 GGTAAAAAAA
Statistics
Matches: 86, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
84 13 0.15
85 56 0.65
86 17 0.20
ACGTcount: A:0.49, C:0.07, G:0.20, T:0.24
Consensus pattern (86 bp):
AGGGGTCTCAATTATAAAAGTGGAAAGTGAGATTAAAAAAAACTTAAAAGTCTAAATAATAAAAT
TAAAAGTAAGATTACAAAATA
Found at i:14944 original size:86 final size:88
Alignment explanation
Indices: 14854--15024 Score: 219
Period size: 86 Copynumber: 2.0 Consensus size: 88
14844 TGGAAATTGA
*
14854 GATTGAAAAAAACTTAAA-AGCATCAATTATAAA-ATTAAAA-GTAAGATT-ACA-AA-ATTAGG
1 GATTGAAAAAAAATTAAAGA-CATCAATTATAAAGA-TAAAAGGTAAGATTGA-ATAATATTAGG
*
14913 AGTCTCAATTATAAAGGTAAAAAAAGG
63 ACT-TCAATTATAAAGGTAAAAAAAGG
* * *
14940 GATTGAAAAAAAATTAGAGACTTCAATTATAAAGATAAAAGGTGAGATTGAATAATATTAGGACT
1 GATTGAAAAAAAATTAAAGACATCAATTATAAAGATAAAAGGTAAGATTGAATAATATTAGGACT
15005 TCAATTATAAAGGTAAAAAA
66 TCAATTATAAAGGTAAAAAA
15025 TAAAAATTAA
Statistics
Matches: 74, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
86 33 0.45
87 10 0.14
88 23 0.31
89 8 0.11
ACGTcount: A:0.53, C:0.06, G:0.15, T:0.26
Consensus pattern (88 bp):
GATTGAAAAAAAATTAAAGACATCAATTATAAAGATAAAAGGTAAGATTGAATAATATTAGGACT
TCAATTATAAAGGTAAAAAAAGG
Found at i:15022 original size:43 final size:44
Alignment explanation
Indices: 14904--15024 Score: 145
Period size: 45 Copynumber: 2.7 Consensus size: 44
14894 GTAAGATTAC
* *
14904 AAAATTAGGAGTCTCAATTATAAAGGTAAAAAAAGGGATTGAAAA
1 AAAATTAGGACT-TCAATTATAAAGGTAAAAAAAGAGATTGAAAA
* *** *
14949 AAAATTAGAGACTTCAATTATAAAGATAAAAGGTGAGATTG-AAT
1 AAAATTAG-GACTTCAATTATAAAGGTAAAAAAAGAGATTGAAAA
*
14993 AATATTAGGACTTCAATTATAAAGGTAAAAAA
1 AAAATTAGGACTTCAATTATAAAGGTAAAAAA
15025 TAAAAATTAA
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
43 21 0.33
44 9 0.14
45 31 0.48
46 3 0.05
ACGTcount: A:0.52, C:0.05, G:0.17, T:0.26
Consensus pattern (44 bp):
AAAATTAGGACTTCAATTATAAAGGTAAAAAAAGAGATTGAAAA
Found at i:15037 original size:86 final size:84
Alignment explanation
Indices: 14859--15064 Score: 199
Period size: 86 Copynumber: 2.4 Consensus size: 84
14849 ATTGAGATTG
* *
14859 AAAAAAACTTAAA-AGCATCAATTATAAA-ATTAAAAGTAAGATTACAAAATTAGGAGTCTCAAT
1 AAAAAAA-TTAAACA-CCTCAATTATAAAGA-TAAAAGTAAGATTACAAAATTAGGACTCTCAAT
***
14922 TATAAAGGTAAAAAAAGGGATT
63 TATAAAGGTAAAAAAAAAAATT
* * * *
14944 GAAAAAAAATTAGAGACTTCAATTATAAAGATAAAAGGTGAGATTGA-ATAATATTAGGACT-TC
1 --AAAAAAATTAAACACCTCAATTATAAAGATAAAA-GTAAGATT-ACA-AA-ATTAGGACTCTC
15007 AATTATAAAGGTAAAAAATAAAAATT
60 AATTATAAAGGTAAAAAA-AAAAATT
15033 -AAAAAATTAAACACCT-AATTATAAAGATAAAA
1 AAAAAAATTAAACACCTCAATTATAAAGATAAAA
15065 ATGTAGGATG
Statistics
Matches: 102, Mismatches: 10, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
85 16 0.16
86 34 0.33
87 17 0.17
88 23 0.23
89 12 0.12
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.25
Consensus pattern (84 bp):
AAAAAAATTAAACACCTCAATTATAAAGATAAAAGTAAGATTACAAAATTAGGACTCTCAATTAT
AAAGGTAAAAAAAAAAATT
Found at i:17526 original size:22 final size:22
Alignment explanation
Indices: 17501--17543 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
17491 CATTTTCTTC
17501 TCCTTCCCATT-TTCTCTCTTTT
1 TCCTTCCCATTCTTC-CTCTTTT
*
17523 TCCTTCTCATTCTTCCTCTTT
1 TCCTTCCCATTCTTCCTCTTT
17544 AAAAGGCCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.05, C:0.37, G:0.00, T:0.58
Consensus pattern (22 bp):
TCCTTCCCATTCTTCCTCTTTT
Found at i:20178 original size:23 final size:23
Alignment explanation
Indices: 20144--20189 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
20134 CCAACCTTTT
*
20144 ACAAAACCTGAAAATAAATCCAA
1 ACAAAACATGAAAATAAATCCAA
20167 ACAAAACATGAAAATAAATCCAA
1 ACAAAACATGAAAATAAATCCAA
20190 CGATTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.63, C:0.20, G:0.04, T:0.13
Consensus pattern (23 bp):
ACAAAACATGAAAATAAATCCAA
Found at i:20235 original size:39 final size:39
Alignment explanation
Indices: 20171--20245 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
20161 ATCCAAACAA
* *
20171 AACATGAAAATAAATCCAACGATTTATTTCCTTTTATAG
1 AACAGGAAAATAAATCCAACAATTTATTTCCTTTTATAG
* *
20210 AACAGGAAAATAAATCTACCAATTTATTTCCTTTTA
1 AACAGGAAAATAAATCCAACAATTTATTTCCTTTTA
20246 CAATCATAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.36
Consensus pattern (39 bp):
AACAGGAAAATAAATCCAACAATTTATTTCCTTTTATAG
Found at i:20839 original size:45 final size:45
Alignment explanation
Indices: 20651--20874 Score: 209
Period size: 45 Copynumber: 5.0 Consensus size: 45
20641 TTACCAACCC
* * ***
20651 AATAATCAAAAGGAACTAATCTTTCTGATTTTAATTTTCGCAATTC
1 AATAATCAAAAGGAACTAATCCTT-TGATTTTAATTTTGGCAACAA
** * * * **
20697 AATAATTGAAAGAAAATAATCCTTTGATTTT-ATTTT-TCAGACCG
1 AATAATCAAAAGGAACTAATCCTTTGATTTTAATTTTGGCA-ACAA
* * *
20741 AGTAATCAAAAGGAACTAATCCTATGATTTCTAATTTTGGCAACTA
1 AATAATCAAAAGGAACTAATCCTTTGATTT-TAATTTTGGCAACAA
* * **
20787 AATAATCAAAATGAACTAATTCTTTGATTTTGTTTTTGGCAACAA
1 AATAATCAAAAGGAACTAATCCTTTGATTTTAATTTTGGCAACAA
* * *
20832 AATAATCAAAAGGAATTAATCCTTTGATTTTACTTTTGTCAAC
1 AATAATCAAAAGGAACTAATCCTTTGATTTTAATTTTGGCAAC
20875 CCAATAATTA
Statistics
Matches: 143, Mismatches: 31, Indels: 9
0.78 0.17 0.05
Matches are distributed among these distances:
43 2 0.01
44 30 0.21
45 57 0.40
46 52 0.36
47 2 0.01
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (45 bp):
AATAATCAAAAGGAACTAATCCTTTGATTTTAATTTTGGCAACAA
Found at i:20869 original size:90 final size:89
Alignment explanation
Indices: 20651--20874 Score: 245
Period size: 90 Copynumber: 2.5 Consensus size: 89
20641 TTACCAACCC
* * * * **
20651 AATAATCAAAAGGAACTAATCTTTCTGATTTTAATTTTCGCAATTCAATAATTGAAAGAAAATAA
1 AATAATCAAAAGGAACTAATCCTT-TGATTTTAATTTTGGCAACTAAATAATCAAAAGAAAATAA
**
20716 TCCTTTGATTTTATTTTTCAGACCG
65 TCCTTTGATTTTATTTTTCAGACAA
* * *
20741 AGTAATCAAAAGGAACTAATCCTATGATTTCTAATTTTGGCAACTAAATAATCAAAATG-AACTA
1 AATAATCAAAAGGAACTAATCCTTTGATTT-TAATTTTGGCAACTAAATAATCAAAA-GAAAATA
* *
20805 ATTCTTTGATTTTGTTTTTGGCA-ACAA
64 ATCCTTTGATTTTATTTTT--CAGACAA
* * *
20832 AATAATCAAAAGGAATTAATCCTTTGATTTTACTTTTGTCAAC
1 AATAATCAAAAGGAACTAATCCTTTGATTTTAATTTTGGCAAC
20875 CCAATAATTA
Statistics
Matches: 112, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
89 6 0.05
90 74 0.66
91 30 0.27
92 2 0.02
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (89 bp):
AATAATCAAAAGGAACTAATCCTTTGATTTTAATTTTGGCAACTAAATAATCAAAAGAAAATAAT
CCTTTGATTTTATTTTTCAGACAA
Found at i:20881 original size:45 final size:45
Alignment explanation
Indices: 20634--20882 Score: 232
Period size: 46 Copynumber: 5.5 Consensus size: 45
20624 GAATTAGTCC
** *
20634 TTTAATTTTACCAACCCAATAATCAAAAGGAACTAATCTTTCTGAT
1 TTTAATTTTGGCAACCCAATAATCAAAAGGAACTAATCCTT-TGAT
* ** ** * *
20680 TTTAATTTTCGCAATTCAATAATTGAAAGAAAATAATCCTTTGAT
1 TTTAATTTTGGCAACCCAATAATCAAAAGGAACTAATCCTTTGAT
* * * *
20725 TTT-ATTTT-TCAGACCGAGTAATCAAAAGGAACTAATCCTATGAT
1 TTTAATTTTGGCA-ACCCAATAATCAAAAGGAACTAATCCTTTGAT
** * *
20769 TTCTAATTTTGGCAACTAAATAATCAAAATGAACTAATTCTTTGAT
1 TT-TAATTTTGGCAACCCAATAATCAAAAGGAACTAATCCTTTGAT
** ** *
20815 TTTGTTTTTGGCAACAAAATAATCAAAAGGAATTAATCCTTTGAT
1 TTTAATTTTGGCAACCCAATAATCAAAAGGAACTAATCCTTTGAT
* *
20860 TTTACTTTTGTCAACCCAATAAT
1 TTTAATTTTGGCAACCCAATAAT
20883 TAAATGGATT
Statistics
Matches: 162, Mismatches: 37, Indels: 9
0.78 0.18 0.04
Matches are distributed among these distances:
43 2 0.01
44 30 0.19
45 63 0.39
46 65 0.40
47 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (45 bp):
TTTAATTTTGGCAACCCAATAATCAAAAGGAACTAATCCTTTGAT
Found at i:22002 original size:145 final size:146
Alignment explanation
Indices: 21756--22044 Score: 357
Period size: 145 Copynumber: 2.0 Consensus size: 146
21746 CATTCCGAAC
* * * * *
21756 GGTCAAAAGTTGCTCAAGACCATCACGAACAACATACTGAAAATTCAGGACGATCAGACGGTGGA
1 GGTCAAAAGTTGCACAAGACCAGCACAAACAACATACTGAAAACTCAAGACGATCAGACGGTGGA
* ** * *
21821 CGGCGGTGGATCGGAGAAAATAAGCCGAACGATTTTTGGCCTCTTTCCT-GCAATCCGGATCTCC
66 CGACGGCAGATCGAAGAAAATAAGCCGAACGATTTTTAGCCT-TTTCCTGGCAATCCGGATCTCC
21885 GATCAACA-TTCAAAAT
130 GATCAACACTTCAAAAT
* **
21901 GGTCAAAAGTTGCACGAGACCAGCACAAACAACATACTGAAAACTCAATTCGATCAGACGGTGGA
1 GGTCAAAAGTTGCACAAGACCAGCACAAACAACATACTGAAAACTCAAGACGATCAGACGGTGGA
* * * * * * * *
21966 CGATGGCAGATCGAAGAAACTAAGTCGAATGGTTTTTAGCCTTTTGCTGGCGATCGGGATCTCCG
66 CGACGGCAGATCGAAGAAAATAAGCCGAACGATTTTTAGCCTTTTCCTGGCAATCCGGATCTCCG
*
22031 ATCAATACTTCAAA
131 ATCAACACTTCAAA
22045 CGTGAAAAGT
Statistics
Matches: 120, Mismatches: 22, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
144 5 0.04
145 109 0.91
146 6 0.05
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.22
Consensus pattern (146 bp):
GGTCAAAAGTTGCACAAGACCAGCACAAACAACATACTGAAAACTCAAGACGATCAGACGGTGGA
CGACGGCAGATCGAAGAAAATAAGCCGAACGATTTTTAGCCTTTTCCTGGCAATCCGGATCTCCG
ATCAACACTTCAAAAT
Found at i:29379 original size:11 final size:10
Alignment explanation
Indices: 29363--29406 Score: 52
Period size: 11 Copynumber: 4.2 Consensus size: 10
29353 ATCCAATCAG
29363 AACAAAAAAGA
1 AACAAAAAA-A
29374 AACAAAAAAA
1 AACAAAAAAA
*
29384 AAAAAAAAAA
1 AACAAAAAAA
*
29394 AAGAGAAAAAA
1 AACA-AAAAAA
29405 AA
1 AA
29407 GGACGATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 13 0.43
11 17 0.57
ACGTcount: A:0.89, C:0.05, G:0.07, T:0.00
Consensus pattern (10 bp):
AACAAAAAAA
Found at i:30478 original size:32 final size:32
Alignment explanation
Indices: 30442--30515 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
30432 GCACTGTTAA
*
30442 AGATTCAACAACAAATGTTGGGGCATATTTGG
1 AGATTCAACAACAAATATTGGGGCATATTTGG
*** *
30474 AGATTCAACATTGAATATTGTGGCATATTTGG
1 AGATTCAACAACAAATATTGGGGCATATTTGG
*
30506 GGATTCAACA
1 AGATTCAACA
30516 TCCTGATGCA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (32 bp):
AGATTCAACAACAAATATTGGGGCATATTTGG
Found at i:30839 original size:43 final size:43
Alignment explanation
Indices: 30790--30913 Score: 158
Period size: 43 Copynumber: 2.9 Consensus size: 43
30780 ATGAAGGCGC
**
30790 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAATG
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACA
* * * *
30833 GATCCACGATTTTAACTCCACGACGGAGGATATCGTGCCCACA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACA
* * * *
30876 CATCCACGGTTTCAACTTCACGACGAAGGAAATCGTAC
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTAC
30914 ACACAAGCAG
Statistics
Matches: 68, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 68 1.00
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (43 bp):
CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACA
Found at i:31303 original size:133 final size:134
Alignment explanation
Indices: 31130--31608 Score: 723
Period size: 133 Copynumber: 3.6 Consensus size: 134
31120 AACTCCATCA
31130 AAGAAGCGGAACAGATTCA-TCTCTTTCAAGATTTGATATTCCCTGAGTGACAGCGAAACAAGTC
1 AAGAAGCGGAACAGA-TCATTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGCGAAACAAGTC
*
31194 TACCATGATTCAATCTTCCCTGAGTGAAAGCGGAATGGATCAACTCATCCAGATCTGATATTCCC
65 TACCATGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACTCATCCAGATCTGATATTCCC
31259 TTCAG
130 TTCAG
* * * *
31264 AAGAAGCGAAACAGATC-TTTTTTTTCAAGACTTGATATTCCCTGAGTGACAGC-AGAACAAGTC
1 AAGAAGCGGAACAGATCATTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGCGA-AACAAGTC
* *
31327 TATCATGATTCAATCTTCACTGAGTGACAGCGGAATGGATCAACTCATCCAGATCTGATATTCCC
65 TACCATGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACTCATCCAGATCTGATATTCCC
*
31392 TTCAA
130 TTCAG
* * * * *
31397 AAGATGTGGAACAGATCATTCTCTTTCAAAATTTGATATTCCCTGAGTGACAGCGGAATAAGTCT
1 AAGAAGCGGAACAGATCATTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGCGAAACAAGTCT
*
31462 ACCA-GATTCAATCTTCCATGAGTGACAGCGGAATGGATCAACTCATCCAGATCTGATATTCCCT
66 ACCATGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACTCATCCAGATCTGATATTCCCT
*
31526 TTAG
131 TCAG
* * *
31530 AAGAAGCGGAACGGATCACTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCT
1 AAGAAGCGGAACAGATCATTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGCGAAACAAGTC-
* *
31595 TGCCACGATTCAAT
65 TACCATGATTCAAT
31609 GGATCAACTT
Statistics
Matches: 310, Mismatches: 29, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
132 1 0.00
133 240 0.77
134 61 0.20
135 8 0.03
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (134 bp):
AAGAAGCGGAACAGATCATTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGCGAAACAAGTCT
ACCATGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACTCATCCAGATCTGATATTCCCT
TCAG
Found at i:31766 original size:111 final size:112
Alignment explanation
Indices: 31493--31830 Score: 531
Period size: 111 Copynumber: 3.0 Consensus size: 112
31483 GTGACAGCGG
* * * * *
31493 AATGGATCAACTCAT-CCAGATCTGATATTCCCTTTAGAAGAAGCGGAACGGATCACTCTCTTTC
1 AATGGATCAACT-TTCCCAGATCTGATATTCCC-TCAGAAGAAGCGAAACAGATCCCTCTCTTTC
31557 AAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTTGCCACGATTC
64 AAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTTGCCACGATTC
31606 AATGGATCAACTTTCCCAGATCTGATATTCCCTCAGAAGAAGC-AGAACAGATCCCTCTCTTTCA
1 AATGGATCAACTTTCCCAGATCTGATATTCCCTCAGAAGAAGCGA-AACAGATCCCTCTCTTTCA
31670 AGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTTG-CACGATTC
65 AGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTTGCCACGATTC
*
31717 AATGGATCAACTTTCCCAGATCTGATATTCCCTCATAAGAAGCGAAACAGATCCCTCTCTTTCAA
1 AATGGATCAACTTTCCCAGATCTGATATTCCCTCAGAAGAAGCGAAACAGATCCCTCTCTTTCAA
* ** *
31782 GATTTGATATTCCATGAGTGACAATGGAACAAGTCTTCCCA-GATTC
66 GATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTTGCCACGATTC
31828 AAT
1 AAT
31831 CTTCCCTGAA
Statistics
Matches: 211, Mismatches: 10, Indels: 10
0.91 0.04 0.04
Matches are distributed among these distances:
111 112 0.53
112 70 0.33
113 29 0.14
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.28
Consensus pattern (112 bp):
AATGGATCAACTTTCCCAGATCTGATATTCCCTCAGAAGAAGCGAAACAGATCCCTCTCTTTCAA
GATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTTGCCACGATTC
Found at i:32873 original size:145 final size:145
Alignment explanation
Indices: 32594--32873 Score: 350
Period size: 145 Copynumber: 1.9 Consensus size: 145
32584 CTCCGATCAC
* * * * *
32594 CATTCCGAACGGTCAAAAGTTGCTCAAGACTATCACGAAAAACATATTGAAAATTCAGGACGATC
1 CATTCCGAACGGTCAAAAGTTGCGCAAGACCAGCACGAAAAACATACTGAAAATTCAGGAAGATC
* ** * * * * *
32659 AGACAGTGGACGGCGGTGGATCGGAGAAAATAAGCTGAACGGTTTTTGGCCTCTTTTCTGGGATT
66 AGACAGTGGACGACGGCAGATCGAAGAAAATAAGCTGAACGGTTTTTAGCCTCTTTGCCGGGATC
32724 GGGATTTTTGCTCAA
131 GGGATTTTTGCTCAA
* * *
32739 CATTCCGAATGGTCAAAATTTGCGCGAGACCAGCAC-AAACAACATACTGAAAATTCAGGAAGAT
1 CATTCCGAACGGTCAAAAGTTGCGCAAGACCAGCACGAAA-AACATACTGAAAATTCAGGAAGAT
* *
32803 GAGACGGTGGACGACGGCAGATCGAAGAAAATAAG-TCGAACGGTTTTTAGCCT-TTTGCCGGCG
65 CAGACAGTGGACGACGGCAGATCGAAGAAAATAAGCT-GAACGGTTTTTAGCCTCTTTGCCGG-G
32866 ATCGGGAT
128 ATCGGGAT
32874 CTCCGATCAA
Statistics
Matches: 114, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
144 10 0.09
145 104 0.91
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (145 bp):
CATTCCGAACGGTCAAAAGTTGCGCAAGACCAGCACGAAAAACATACTGAAAATTCAGGAAGATC
AGACAGTGGACGACGGCAGATCGAAGAAAATAAGCTGAACGGTTTTTAGCCTCTTTGCCGGGATC
GGGATTTTTGCTCAA
Found at i:32954 original size:145 final size:146
Alignment explanation
Indices: 32776--33103 Score: 346
Period size: 146 Copynumber: 2.3 Consensus size: 146
32766 GACCAGCACA
* * * *
32776 AACAACATACTGAAAATTCAGGAA-GAT-GAGACGGTGGACGACGGCAG-ATCGAAGAAAATAAG
1 AACAACATACTGAAATTTCA-GAACAATCG-GACGGTGGACGACGG-AGAATCGAAGAAAACAAA
* * * * *
32838 TCGA-ACGGTTTTTAGCCTTTTGCCGGCGATCGGGATC-TCCGATCAATACTT-CAAACGCTGAA
63 TCCAGACGGTTTTTAGCCTCTCGCCGGCGATC-GGAACGTCCGATCAATA-TTCCAAACGCTCAA
* * *
32900 AAGTTGTGTAATGTCAATACG
126 AAGTTGCGCAATGTCAACACG
* * ** * *
32921 AACAGCATACTGAAATTTCATG-ACAATCGGACGGTAGACGGTGGTGAATCGGAGAAAACAAATC
1 AACAACATACTGAAATTTCA-GAACAATCGGACGGTGGACGACGGAGAATCGAAGAAAACAAATC
* * * *
32985 CAGACGGTTTTTGGCCTCTCGCCGGTGATCGGAACGTCCGATCAATATTCCGAACGGTCAAAAGT
65 CAGACGGTTTTTAGCCTCTCGCCGGCGATCGGAACGTCCGATCAATATTCCAAACGCTCAAAAGT
*
33050 TGCGCGATGTCAACACG
130 TGCGCAATGTCAACACG
33067 AACAACATACTGAAATTTCAGAACAATCGGACGGTGG
1 AACAACATACTGAAATTTCAGAACAATCGGACGGTGG
33104 TACGGCAGCG
Statistics
Matches: 150, Mismatches: 26, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
144 2 0.01
145 55 0.37
146 93 0.62
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22
Consensus pattern (146 bp):
AACAACATACTGAAATTTCAGAACAATCGGACGGTGGACGACGGAGAATCGAAGAAAACAAATCC
AGACGGTTTTTAGCCTCTCGCCGGCGATCGGAACGTCCGATCAATATTCCAAACGCTCAAAAGTT
GCGCAATGTCAACACG
Found at i:41385 original size:21 final size:21
Alignment explanation
Indices: 41359--41398 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
41349 CCCCCTTTGA
*
41359 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
41380 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
41399 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:43677 original size:13 final size:13
Alignment explanation
Indices: 43659--43710 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 13
43649 GTAATTTCTA
43659 ATTTCAAAACTTG
1 ATTTCAAAACTTG
* *
43672 ATTTCAAAATTTTTCTA
1 ATTTCAAAA---CT-TG
43689 ATTTCAAAACTTG
1 ATTTCAAAACTTG
43702 ATTTCAAAA
1 ATTTCAAAA
43711 ATCTTAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
13 19 0.61
14 1 0.03
16 1 0.03
17 10 0.32
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.42
Consensus pattern (13 bp):
ATTTCAAAACTTG
Found at i:43687 original size:30 final size:30
Alignment explanation
Indices: 43653--43710 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
43643 GGGGGAGTAA
43653 TTTCTAATTTCAAAACTTGATTTCAAAATT
1 TTTCTAATTTCAAAACTTGATTTCAAAATT
43683 TTTCTAATTTCAAAACTTGATTTCAAAA
1 TTTCTAATTTCAAAACTTGATTTCAAAA
43711 ATCTTAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.38, C:0.14, G:0.03, T:0.45
Consensus pattern (30 bp):
TTTCTAATTTCAAAACTTGATTTCAAAATT
Found at i:47000 original size:21 final size:20
Alignment explanation
Indices: 46914--47071 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
46904 AAATGACCAA
**
46914 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
46933 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
** *
46953 CAAAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
46973 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
46994 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
47015 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
47035 CCAAAATCACAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
47056 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
47072 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 42 0.40
21 46 0.44
ACGTcount: A:0.40, C:0.25, G:0.16, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:47100 original size:20 final size:20
Alignment explanation
Indices: 47058--47307 Score: 247
Period size: 20 Copynumber: 12.5 Consensus size: 20
47048 GCGAATATGA
* *
47058 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
*
47078 AAATCGCAACGCCTATCCGT
1 AAATCGCAACGCGTATCCGT
*
47098 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
47118 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
47138 AAATCACAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
47158 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
47178 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
47198 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
47218 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
47238 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
47258 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
47278 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
47298 AAATCACAAC
1 AAATCGCAAC
47308 ACTGAAATTT
Statistics
Matches: 192, Mismatches: 31, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
19 1 0.01
20 189 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:48029 original size:24 final size:24
Alignment explanation
Indices: 47990--48036 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
47980 AAATTTGGTC
47990 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
48014 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
48037 GATGTTTCAG
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:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:50793 original size:14 final size:14
Alignment explanation
Indices: 50774--50830 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
50764 GCGAAATGAA
*
50774 AATCGCAACGACAG
1 AATCGCAACGAAAG
50788 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
50805 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
50821 AATCGCAACG
1 AATCGCAACG
50831 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:50801 original size:33 final size:33
Alignment explanation
Indices: 50755--50847 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
50745 GCGAAACCAA
*
50755 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
50788 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
50821 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
50848 TACGATTTTG
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:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:50812 original size:19 final size:19
Alignment explanation
Indices: 50718--50847 Score: 127
Period size: 19 Copynumber: 7.3 Consensus size: 19
50708 TAGTTTACTT
* *
50718 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
50738 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
50757 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
50776 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
50790 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
50809 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
50823 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
50842 TCGCAA
1 TCGCAA
50848 TACGATTTTG
Statistics
Matches: 93, Mismatches: 7, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.17
16 11 0.12
17 11 0.12
19 43 0.46
20 12 0.13
ACGTcount: A:0.47, C:0.24, G:0.18, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:50872 original size:19 final size:19
Alignment explanation
Indices: 50850--50976 Score: 121
Period size: 19 Copynumber: 7.2 Consensus size: 19
50840 AATCGCAATA
50850 CGATTTTGGTTTCGCGTTG
1 CGATTTTGGTTTCGCGTTG
*
50869 CGATCTT-G--T--CGTTG
1 CGATTTTGGTTTCGCGTTG
50883 CGATTTTGGTTTCGCGTTG
1 CGATTTTGGTTTCGCGTTG
*
50902 CGATTAT-G--T--CGTTG
1 CGATTTTGGTTTCGCGTTG
**
50916 CGATTTTCATTTCGCGTTG
1 CGATTTTGGTTTCGCGTTG
50935 CGATTTTGGTTTCGCGTTG
1 CGATTTTGGTTTCGCGTTG
* *
50954 CGATTTTAAGTTTCGTGTTG
1 CGATTTT-GGTTTCGCGTTG
50974 CGA
1 CGA
50977 AAGTAAACTA
Statistics
Matches: 88, Mismatches: 9, Indels: 21
0.75 0.08 0.18
Matches are distributed among these distances:
14 22 0.25
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 46 0.52
20 13 0.15
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.46
Consensus pattern (19 bp):
CGATTTTGGTTTCGCGTTG
Found at i:50892 original size:33 final size:33
Alignment explanation
Indices: 50850--50939 Score: 146
Period size: 33 Copynumber: 2.7 Consensus size: 33
50840 AATCGCAATA
50850 CGATTTTGGTTTCGCGTTGCGATCT-TGTCGTTG
1 CGATTTTGGTTTCGCGTTGCGAT-TATGTCGTTG
50883 CGATTTTGGTTTCGCGTTGCGATTATGTCGTTG
1 CGATTTTGGTTTCGCGTTGCGATTATGTCGTTG
**
50916 CGATTTTCATTTCGCGTTGCGATT
1 CGATTTTGGTTTCGCGTTGCGATT
50940 TTGGTTTCGC
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 1 0.02
33 53 0.98
ACGTcount: A:0.09, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
CGATTTTGGTTTCGCGTTGCGATTATGTCGTTG
Found at i:51140 original size:93 final size:93
Alignment explanation
Indices: 51024--51491 Score: 913
Period size: 93 Copynumber: 5.1 Consensus size: 93
51014 ATGGATTGCA
51024 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
51088 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
51116 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
51181 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
51209 TTACTTTCAACC-AAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
51273 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
51301 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
51366 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
51394 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
51459 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
51487 TTACT
1 TTACT
51492 AAGCAATCTA
Statistics
Matches: 373, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
92 96 0.26
93 277 0.74
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:51348 original size:185 final size:186
Alignment explanation
Indices: 51024--51491 Score: 913
Period size: 185 Copynumber: 2.5 Consensus size: 186
51014 ATGGATTGCA
51024 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
51088 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
51153 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
51209 TTACTTTCAACC-AAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
51273 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
51338 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
51394 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
51459 TAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACT
51492 AAGCAATCTA
Statistics
Matches: 280, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
185 189 0.68
186 91 0.32
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:53214 original size:14 final size:14
Alignment explanation
Indices: 53195--53284 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
53185 TTGAAATGAA
53195 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
53209 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
53228 AATCGCAACTAGAG
1 AATCGCAACGAGAG
*
53242 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
53261 AATCGCAACGAGAG
1 AATCGCAACGAGAG
53275 AATCGCAACG
1 AATCGCAACG
53285 CGAAATGAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
14 30 0.50
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 20 0.33
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.10
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:53227 original size:33 final size:33
Alignment explanation
Indices: 53187--53301 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
53177 TCTTTTGGTT
53187 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
53220 GAAATGAAAATCGCAACTAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
53253 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
53286 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
53302 TGCGATTTTG
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.47, C:0.20, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:53233 original size:19 final size:19
Alignment explanation
Indices: 53209--53306 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
53199 GCAACGAGAG
53209 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
* *
53228 AATCGCAA--C--TA-GAG
1 AATCGCAACGCGAAATGAA
53242 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
53261 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
53275 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
53294 AATCGCAATGCGA
1 AATCGCAACGCGA
53307 TTTTGGTTTC
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 32 0.52
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:53337 original size:14 final size:14
Alignment explanation
Indices: 53318--53374 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
53308 TTTGGTTTCG
53318 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
53332 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
53351 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
53365 CGTTGCGATT
1 CGTTGCGATT
53375 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:53350 original size:33 final size:33
Alignment explanation
Indices: 53302--53382 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
53292 AAAATCGCAA
**
53302 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
53335 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
53368 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
53383 TCTCGTTGCG
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:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:53385 original size:21 final size:21
Alignment explanation
Indices: 53359--53434 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
53349 CGCGTTGCGA
53359 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
53380 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
53400 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
53421 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
53435 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:53415 original size:41 final size:41
Alignment explanation
Indices: 53358--53435 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
53348 TCGCGTTGCG
*
53358 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
53399 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
53436 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:53556 original size:33 final size:33
Alignment explanation
Indices: 53514--53584 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
53504 AATACTAACT
* *
53514 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCAAAA
* *
53547 TGAAAATCGCAACGACAGAATCGTAACGCAAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCAAAA
53580 TGAAA
1 TGAAA
53585 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.49, C:0.18, G:0.21, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCAAAA
Found at i:53817 original size:22 final size:21
Alignment explanation
Indices: 53766--53819 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
53756 TGGTTGTGAG
**
53766 GGATTTCGCCGGAGATGGGAC
1 GGATTTCTTCGGAGATGGGAC
**
53787 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGAT-GGGAC
53809 GGATTTCTTCG
1 GGATTTCTTCG
53820 CCGTAGAGAG
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.20, C:0.17, G:0.39, T:0.24
Consensus pattern (21 bp):
GGATTTCTTCGGAGATGGGAC
Found at i:53991 original size:20 final size:20
Alignment explanation
Indices: 53966--54119 Score: 159
Period size: 20 Copynumber: 7.7 Consensus size: 20
53956 CTTTAAATAT
53966 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
53986 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
54008 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
54027 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
54047 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
54067 GGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
54087 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
54107 CGCGTTGCGATTT
1 CGCGTTGCGATTT
54120 TGGAAAATCG
Statistics
Matches: 111, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
19 2 0.02
20 92 0.83
21 15 0.14
22 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:54093 original size:40 final size:40
Alignment explanation
Indices: 53965--54119 Score: 177
Period size: 40 Copynumber: 3.9 Consensus size: 40
53955 GCTTTAAATA
*
53965 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTGT
** * *
54006 TATCGTTGCGATTTACGGATACGCGTTGCGATATACG-GAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
* * *
54046 ACACGTTGCGATTTACGGATAGGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
* ** *
54086 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTT
54120 TGGAAAATCG
Statistics
Matches: 94, Mismatches: 18, Indels: 5
0.80 0.15 0.04
Matches are distributed among these distances:
40 64 0.68
41 30 0.32
ACGTcount: A:0.18, C:0.17, G:0.27, T:0.37
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
Found at i:54136 original size:21 final size:21
Alignment explanation
Indices: 54106--54188 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
54096 ATTTTCATAT
*
54106 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
54127 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
54148 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
54169 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
54189 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:54179 original size:42 final size:43
Alignment explanation
Indices: 54086--54184 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
54076 ATTTATGTGT
* *
54086 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
54127 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
54169 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
54185 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:55910 original size:58 final size:57
Alignment explanation
Indices: 55787--55913 Score: 164
Period size: 58 Copynumber: 2.2 Consensus size: 57
55777 TAGATCAAAT
* * ** * *
55787 ATTCTCAAGGAAATAAATTCAACTATTTCTTTTCTTACAAAGTTAGAGTTGTTTAAT
1 ATTCTCAAGGAAATAAATTCAACAATTTCTTTTCTTACAAAGTTAGAATCATTCAAG
* * *
55844 ATTTTCAAGGAAATAAATTTAACAATTTATTTTTCTTACAAAGTTAGAATCATTCAAG
1 ATTCTCAAGGAAATAAATTCAACAATTT-CTTTTCTTACAAAGTTAGAATCATTCAAG
55902 ATTCTCAAGGAA
1 ATTCTCAAGGAA
55914 GTTATTTAAG
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
57 25 0.42
58 34 0.58
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (57 bp):
ATTCTCAAGGAAATAAATTCAACAATTTCTTTTCTTACAAAGTTAGAATCATTCAAG
Found at i:56019 original size:57 final size:58
Alignment explanation
Indices: 55915--56087 Score: 235
Period size: 57 Copynumber: 3.0 Consensus size: 58
55905 CTCAAGGAAG
* * * *
55915 TTATTTAAGATTTTCAAGAAAATAAATTCAACAATTT-TTATT-TTTACAAAGTTAGAA
1 TTATTCAAGATTATAAAGGAAATAAATTCAACAATTTATT-TTCTTTACAAAGTTAGAA
* *
55972 TTATTCAAGATTCT-AAGGAAATAAACTCAACAATTTATTTTCTTTACAAAGTTAGAA
1 TTATTCAAGATTATAAAGGAAATAAATTCAACAATTTATTTTCTTTACAAAGTTAGAA
* * *
56029 TCATTCAAGATTATAAAGGAAATAAATTCAACAATTTATTTTCCTTACGAAGTTAGAA
1 TTATTCAAGATTATAAAGGAAATAAATTCAACAATTTATTTTCTTTACAAAGTTAGAA
56087 T
1 T
56088 CAACGCAAGA
Statistics
Matches: 104, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
56 22 0.21
57 41 0.39
58 41 0.39
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.38
Consensus pattern (58 bp):
TTATTCAAGATTATAAAGGAAATAAATTCAACAATTTATTTTCTTTACAAAGTTAGAA
Found at i:56036 original size:136 final size:137
Alignment explanation
Indices: 55791--56049 Score: 371
Period size: 136 Copynumber: 1.9 Consensus size: 137
55781 TCAAATATTC
* * * * * * *
55791 TCAAGGAAATAAATTCAACTATTTCTTTTCTTACAAAGTTAGAGTTGTTTAATATTTTCAAGGAA
1 TCAAGAAAATAAATTCAACAATTTCTTTTCTTACAAAGTTAGAATTATTCAAGATTCTCAAGGAA
* * * *
55856 ATAAATTTAACAATTTATTTTTCTTACAAAGTTAGAATCATTCAAGATTCTCAAGGAAGTTATTT
66 ATAAACTCAACAATTTATTTTTCTTACAAAGTTAGAATCATTCAAGATTATAAAGGAAGTTATTT
55921 AAGATTT
131 AAGATTT
*
55928 TCAAGAAAATAAATTCAACAATTT-TTATTTTTACAAAGTTAGAATTATTCAAGATTCT-AAGGA
1 TCAAGAAAATAAATTCAACAATTTCTT-TTCTTACAAAGTTAGAATTATTCAAGATTCTCAAGGA
55991 AATAAACTCAACAATTTA-TTTTCTTTACAAAGTTAGAATCATTCAAGATTATAAAGGAA
65 AATAAACTCAACAATTTATTTTTC-TTACAAAGTTAGAATCATTCAAGATTATAAAGGAA
56050 ATAAATTCAA
Statistics
Matches: 108, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
135 5 0.05
136 56 0.52
137 47 0.44
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.38
Consensus pattern (137 bp):
TCAAGAAAATAAATTCAACAATTTCTTTTCTTACAAAGTTAGAATTATTCAAGATTCTCAAGGAA
ATAAACTCAACAATTTATTTTTCTTACAAAGTTAGAATCATTCAAGATTATAAAGGAAGTTATTT
AAGATTT
Found at i:56070 original size:58 final size:57
Alignment explanation
Indices: 55934--56089 Score: 235
Period size: 58 Copynumber: 2.7 Consensus size: 57
55924 ATTTTCAAGA
* *
55934 AAATAAATTCAACAATTT-TTATT-TTTACAAAGTTAGAATTATTCAAGATTCTAAGG
1 AAATAAATTCAACAATTTATT-TTCTTTACAAAGTTAGAATCATTCAAGATTATAAGG
*
55990 AAATAAACTCAACAATTTATTTTCTTTACAAAGTTAGAATCATTCAAGATTATAAAGG
1 AAATAAATTCAACAATTTATTTTCTTTACAAAGTTAGAATCATTCAAGATTAT-AAGG
* *
56048 AAATAAATTCAACAATTTATTTTCCTTACGAAGTTAGAATCA
1 AAATAAATTCAACAATTTATTTTCTTTACAAAGTTAGAATCA
56090 ACGCAAGATT
Statistics
Matches: 91, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
56 19 0.21
57 29 0.32
58 43 0.47
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.37
Consensus pattern (57 bp):
AAATAAATTCAACAATTTATTTTCTTTACAAAGTTAGAATCATTCAAGATTATAAGG
Found at i:58815 original size:20 final size:20
Alignment explanation
Indices: 58773--58815 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
58763 CTATTTTCAT
* *
58773 TTTTTAATTTTGAAATACCA
1 TTTTTAATTTTGAAAAACAA
58793 TTTTTATATTTT-AAAAACAA
1 TTTTTA-ATTTTGAAAAACAA
58813 TTT
1 TTT
58816 CTCATAATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.53
Consensus pattern (20 bp):
TTTTTAATTTTGAAAAACAA
Found at i:60554 original size:124 final size:124
Alignment explanation
Indices: 60334--60583 Score: 344
Period size: 124 Copynumber: 2.0 Consensus size: 124
60324 AAACTTACAA
* *
60334 GAAAATCCTCACAAGGCAAGATATTTGCACAATTATAGAATAAAGAAAGAACACTAAAGAATAAT
1 GAAAAACCTCACAAGGCAAGATATTTGCACAATTATAGAACAAAGAAAGAACACTAAAGAATAAT
* * *
60399 ACAATTGAGCACAATAAGTGTTCTTGAAAGCAAAAATGAATATTGAATG-AAATAGGCTT
66 AAAAATGAGCACAATAAGTGTTCTTGAAAGC-AAAATGAATATTGAAGGAAAATAGGCTT
* * * *
60458 GAAAAACCTCACAAGGTAAGATGTTTGCACAATTCTAGAAC-AAGAAAATAACACTAAA-AATGA
1 GAAAAACCTCACAAGGCAAGATATTTGCACAATTATAGAACAAAG-AAAGAACACTAAAGAAT-A
* * *
60521 TTAAAAATGAGCACAATATGTGTTCTTGAAAGCAAAATGAATATTGAAGGAAAATTGGCTT
64 ATAAAAATGAGCACAATAAGTGTTCTTGAAAGCAAAATGAATATTGAAGGAAAATAGGCTT
60582 GA
1 GA
60584 TTTTCACAAA
Statistics
Matches: 111, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
123 22 0.20
124 89 0.80
ACGTcount: A:0.48, C:0.12, G:0.17, T:0.24
Consensus pattern (124 bp):
GAAAAACCTCACAAGGCAAGATATTTGCACAATTATAGAACAAAGAAAGAACACTAAAGAATAAT
AAAAATGAGCACAATAAGTGTTCTTGAAAGCAAAATGAATATTGAAGGAAAATAGGCTT
Found at i:60864 original size:21 final size:20
Alignment explanation
Indices: 60838--60912 Score: 73
Period size: 22 Copynumber: 3.6 Consensus size: 20
60828 ATATGCCTGA
*
60838 GGGTATCGGTACCTCCTGAGG
1 GGGTATCGATACCT-CTGAGG
60859 GGGTATCGATACCAT-TGCATGG
1 GGGTATCGATACC-TCTG-A-GG
*
60881 GTGTATCGATACCTCTG-GG
1 GGGTATCGATACCTCTGAGG
*
60900 GGGTATCGGTACC
1 GGGTATCGATACC
60913 ATCCGAGCAT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
19 13 0.28
20 2 0.04
21 14 0.30
22 17 0.37
ACGTcount: A:0.17, C:0.21, G:0.35, T:0.27
Consensus pattern (20 bp):
GGGTATCGATACCTCTGAGG
Found at i:66556 original size:20 final size:22
Alignment explanation
Indices: 66505--66561 Score: 75
Period size: 20 Copynumber: 2.7 Consensus size: 22
66495 CCAAAATGTA
*
66505 CTCGAGTATCGATACTAAGCCT
1 CTCGAGTATCGATACTAACCCT
66527 CTCG-GTATCGATACT-ACCCT
1 CTCGAGTATCGATACTAACCCT
*
66547 -TTGAGTATCGATACT
1 CTCGAGTATCGATACT
66562 CATATCAGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.06
20 15 0.47
21 11 0.34
22 4 0.12
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.32
Consensus pattern (22 bp):
CTCGAGTATCGATACTAACCCT
Found at i:73743 original size:81 final size:82
Alignment explanation
Indices: 73589--73744 Score: 197
Period size: 81 Copynumber: 1.9 Consensus size: 82
73579 GATACCAGGA
* * * ** * * *
73589 AACATCAAATCTAAAATTGGTATTGATACTGAAATTGGGGTATCGATACCATAGTATGGTAGTAT
1 AACATCAAACCTAAAATTGGTATCGATACTCAAAAGGGGGTATCGATACCATAGCATAGAAGTAT
73654 CAATACCATGATAAGGC
66 CAATACCATGATAAGGC
* *
73671 AACATCAAACCTAAAATTGGTATCGATAC-CAAAAGGGGGTATTGGTACCATAGCATAGAAGTAT
1 AACATCAAACCTAAAATTGGTATCGATACTCAAAAGGGGGTATCGATACCATAGCATAGAAGTAT
**
73735 CGGTACCATG
66 CAATACCATG
73745 GCAATAGTAT
Statistics
Matches: 62, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
81 35 0.56
82 27 0.44
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (82 bp):
AACATCAAACCTAAAATTGGTATCGATACTCAAAAGGGGGTATCGATACCATAGCATAGAAGTAT
CAATACCATGATAAGGC
Found at i:74158 original size:54 final size:53
Alignment explanation
Indices: 74084--74256 Score: 249
Period size: 54 Copynumber: 3.2 Consensus size: 53
74074 TACCAAATAG
* *
74084 GCACTAAGT-TGTATTTCACAGAATTCATCCTATGTGGGTGAATAATCGTTTC
1 GCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAATCGTTTC
74136 AGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAATCGTTTC
1 -GCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAATCGTTTC
** * *
74190 GACACTAAGTGTGCATTTCATGGAATTCATCTTATGTGGATGAATAACCGTTTC
1 G-CACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAATCGTTTC
*
74244 GGCACTATGTGTG
1 -GCACTAAGTGTG
74257 TAAAGCACGA
Statistics
Matches: 110, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
53 10 0.09
54 99 0.90
55 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (53 bp):
GCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAATCGTTTC
Found at i:74287 original size:108 final size:107
Alignment explanation
Indices: 74085--74288 Score: 239
Period size: 108 Copynumber: 1.9 Consensus size: 107
74075 ACCAAATAGG
* * *
74085 CACTAAGTTGTATTTCACAGAATTCATCCTATGTGGGTGAATAATCGTTTCAGCACTAAGTGTGC
1 CACTAAGTTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCAGCACTAAGTGTGC
*** **
74150 ATTTCACAGAATTCATCCTATGTGGATGAATAATCGTTTCGA
66 AAAGCACAGAATTCATAATATGTGGATGAATAATCGTTTCGA
** * * *
74192 CACTAAGTGTGCATTTCATGGAATTCATCTTATGTGGATGAATAACCGTTTCGGCACTATGTGTG
1 CACTAAGT-TGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCAGCACTAAGTGTG
* * *
74257 TAAAGCAC-GAAATTCATAATTTGTGTATGAAT
65 CAAAGCACAG-AATTCATAATATGTGGATGAAT
74289 TTCTGTATAG
Statistics
Matches: 79, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
107 9 0.11
108 70 0.89
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (107 bp):
CACTAAGTTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCAGCACTAAGTGTGC
AAAGCACAGAATTCATAATATGTGGATGAATAATCGTTTCGA
Found at i:74452 original size:58 final size:59
Alignment explanation
Indices: 74265--74475 Score: 282
Period size: 59 Copynumber: 3.6 Consensus size: 59
74255 TGTAAAGCAC
* ** *
74265 GAAATTCATAATTTGTGTATGAATTTCTGTATAGGGCACTTCGTGTGCTAAAAGGTTAA
1 GAAATTCATACTAAGTGTATGAATTTCTGTATAGGGCACTTCGTGTGCTAAAATGTTAA
* *
74324 TAAATTCATACTAAGTGTATGAATTTCTGTATAGGGCACTTCGTTTGCTAAAATGTTAA
1 GAAATTCATACTAAGTGTATGAATTTCTGTATAGGGCACTTCGTGTGCTAAAATGTTAA
* * * * **
74383 GAAATTTATACTAAGTGTATGAATTT-TCGTATTGGGTACTTTGTGTG-TAAAATAATAA
1 GAAATTCATACTAAGTGTATGAATTTCT-GTATAGGGCACTTCGTGTGCTAAAATGTTAA
*
74441 GAAATTCATACTAAATGTATGAATTTCTGTATAGG
1 GAAATTCATACTAAGTGTATGAATTTCTGTATAGG
74476 AAATATATGT
Statistics
Matches: 133, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
58 40 0.30
59 93 0.70
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.39
Consensus pattern (59 bp):
GAAATTCATACTAAGTGTATGAATTTCTGTATAGGGCACTTCGTGTGCTAAAATGTTAA
Found at i:74505 original size:57 final size:58
Alignment explanation
Indices: 74380--74507 Score: 145
Period size: 57 Copynumber: 2.2 Consensus size: 58
74370 GCTAAAATGT
* * * * * * *
74380 TAAGAAATTTATACTAAGTGTATGAATTTTCGTATTGGGTACTTTGTGTGTAAAATAA
1 TAAGAAATTCATACTAAATGTATGAATTTTCGTATTAGGAAATATATGTGTAAAATAA
*
74438 TAAGAAATTCATACTAAATGTATGAA-TTTCTGTA-TAGGAAATATATGTGTATAAA-CA
1 TAAGAAATTCATACTAAATGTATGAATTTTC-GTATTAGGAAATATATGTGTA-AAATAA
74495 TAAGAAATTCATA
1 TAAGAAATTCATA
74508 ATAAGGAAAT
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
57 30 0.50
58 30 0.50
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.38
Consensus pattern (58 bp):
TAAGAAATTCATACTAAATGTATGAATTTTCGTATTAGGAAATATATGTGTAAAATAA
Found at i:74931 original size:68 final size:68
Alignment explanation
Indices: 74822--75024 Score: 318
Period size: 68 Copynumber: 3.0 Consensus size: 68
74812 CGGTTAAAGG
* *
74822 CCTAACTGTGCATTTGACAGAAAGGTTTCAATTTTGCCATTTAGATGAAAGGCTAAGTGCCTTTG
1 CCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCATTTAGATGAAAGGCTAAGTGCCTTTG
74887 AGA
66 AGA
*
74890 CCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCATTTAGAAGAAAGGCTAAGTGCCTTTG
1 CCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCATTTAGATGAAAGGCTAAGTGCCTTTG
*
74955 AGG
66 AGA
* * * *
74958 CCTAGA-TGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATGCCTTT
1 CCTA-ACTGTGCATTTGACAGAAAGGTGTCAATTATGCCATTTAGATGAAAGGCTAAGTGCCTTT
75022 GAG
65 GAG
75025 TAAAAGACTA
Statistics
Matches: 125, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
68 124 0.99
69 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.30
Consensus pattern (68 bp):
CCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCATTTAGATGAAAGGCTAAGTGCCTTTG
AGA
Found at i:75143 original size:45 final size:45
Alignment explanation
Indices: 75040--75191 Score: 160
Period size: 45 Copynumber: 3.3 Consensus size: 45
75030 GACTAGATGT
* *
75040 ATAACAATGTATAATGGTGTTTAAAAGGCATTAAAAGATGCCATAA
1 ATAA-AATGTATAATGGTGTATAAAAGGCATGAAAAGATGCCATAA
* * * * *
75086 CTGAAATATATAACGGTGTATAAAAGGCATGAAATGATGCCATAA
1 ATAAAATGTATAATGGTGTATAAAAGGCATGAAAAGATGCCATAA
* * ** *
75131 ATAAAATGTATAATAGTATATAAAAAGGCATGAACGGTTGCCATAA
1 ATAAAATGTATAATGGTGTAT-AAAAGGCATGAAAAGATGCCATAA
*
75177 ATAAAAATGCATAAT
1 AT-AAAATGTATAAT
75192 TATGCATTAT
Statistics
Matches: 87, Mismatches: 17, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
45 51 0.59
46 25 0.29
47 11 0.13
ACGTcount: A:0.47, C:0.09, G:0.17, T:0.26
Consensus pattern (45 bp):
ATAAAATGTATAATGGTGTATAAAAGGCATGAAAAGATGCCATAA
Found at i:78314 original size:2 final size:2
Alignment explanation
Indices: 78307--78334 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
78297 CAATTTTCTG
78307 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
78335 GTTTATCGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.