Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 200 of 310
Found at i:65422977 original size:93 final size:93
Alignment explanation
Indices: 65422866--65423092 Score: 409
Period size: 93 Copynumber: 2.4 Consensus size: 93
65422856 TGGATATTTG
* *
65422866 GGCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCAAACTCGTTGAG
*
65422931 TTGAGTCCGAGTTTGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
65422959 GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCAAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCAAACTCGTTGAG
65423024 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
65423052 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
65423093 GCGAGTTACA
Statistics
Matches: 128, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 128 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCAAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:65423084 original size:47 final size:47
Alignment explanation
Indices: 65422916--65423085 Score: 215
Period size: 47 Copynumber: 3.6 Consensus size: 47
65422906 GATGCGAACG
*
65422916 TCCGAACTCGTTGAGTTGAGTCCGAGTTTGTGAGATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
* * * *
65422963 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---G--
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCA
*
65423009 TCCAAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
65423056 TCCGAACTCGTTGAGTTGAGTCCGAGTTCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCG
65423086 CTTATGGGCG
Statistics
Matches: 103, Mismatches: 11, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
42 3 0.03
43 4 0.04
45 3 0.03
46 27 0.26
47 56 0.54
48 3 0.03
50 4 0.04
51 3 0.03
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (47 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
Found at i:65425148 original size:19 final size:19
Alignment explanation
Indices: 65425124--65425171 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
65425114 TGTGTCACGC
65425124 CCGTGTGCAAGTGCTCAAG
1 CCGTGTGCAAGTGCTCAAG
65425143 CCGTGTGCAAGTGCTCAAG
1 CCGTGTGCAAGTGCTCAAG
*
65425162 CTGTGTGCAA
1 CCGTGTGCAA
65425172 TTCTAACTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.31, T:0.23
Consensus pattern (19 bp):
CCGTGTGCAAGTGCTCAAG
Found at i:65432992 original size:273 final size:273
Alignment explanation
Indices: 65432265--65433084 Score: 1480
Period size: 273 Copynumber: 3.0 Consensus size: 273
65432255 CGCCTTACCT
*
65432265 CTCCAAGCCTGTCGATCTTCATATAAATGACAAGAGAGAGGAATACTCATGACTTTTGTTGCCTC
1 CTCCAAGCCTGTCGATCTTCATATAAATGACAAGAGAGAAGAATACTCATGACTTTTGTTGCCTC
* *
65432330 TTCAGTAGACATAAACTAGTAATTACATCCTCGTTCCACTTCCTCGAATTTTGATTTATAAGTTC
66 TTCAATAGACATAAACTAGTAATTACATCCTCGTTCCACTTCCTCGAATTTTGATATATAAGTTC
* * * *
65432395 AGGAACCAATCTTAGATTTTGACCCATTACATTTCTTTGAAGCTCATAGTTCTCCAAGTTTGGCA
131 AGAAACCAATCTTAGATTTTAACCCGTTACATTTCTTTGAAGCTCATAGTTCTCGAAGTTTGGCA
* * * * *
65432460 CCCAGGCCTCATTCCATATCAATATTCTAGTTCCCATTCCCATCCTCCAACACATGCCTAATTGG
196 CCCAGGCATCATTTCATATCGATATTCTAGTTCTCATTCCCACCCTCCAACACATGCCTAATTGG
65432525 AGCAATCCTTTCG
261 AGCAATCCTTTCG
65432538 CTCCAAGCCTGTCGATCTTCATATAAATGACAAGAGAGAAGAATACTCAT-ACTTTTGTTGCCTC
1 CTCCAAGCCTGTCGATCTTCATATAAATGACAAGAGAGAAGAATACTCATGACTTTTGTTGCCTC
65432602 TTCAATAGACATAAACTAGTAATTACATCCTCGTTCCACTTCCTCGAATTTTGATATATAAGTTC
66 TTCAATAGACATAAACTAGTAATTACATCCTCGTTCCACTTCCTCGAATTTTGATATATAAGTTC
65432667 AGAAACCAATCTTAGATTTTAACCCGTTACATTTCTTTGAAGCTCATAGTTCTCGAAGTTTGGCA
131 AGAAACCAATCTTAGATTTTAACCCGTTACATTTCTTTGAAGCTCATAGTTCTCGAAGTTTGGCA
65432732 CCCAGGCATCATTTCATATCGATATTCTAGTTCTCATTCCCACCCTCCAACACATGCCTAATTGG
196 CCCAGGCATCATTTCATATCGATATTCTAGTTCTCATTCCCACCCTCCAACACATGCCTAATTGG
65432797 AGCAATCCTTTCG
261 AGCAATCCTTTCG
* * *
65432810 CTCCAAGCCTGTCGATCTTCATATAAATGATAGGAGAGAAGACTACTCATGACTTTTGTTGCCTC
1 CTCCAAGCCTGTCGATCTTCATATAAATGACAAGAGAGAAGAATACTCATGACTTTTGTTGCCTC
* *
65432875 TTCAATAGACATAAACTAGTAATTACATCCTCATTCTACTTCCTCGAATTTTGATATATAAGTTC
66 TTCAATAGACATAAACTAGTAATTACATCCTCGTTCCACTTCCTCGAATTTTGATATATAAGTTC
65432940 AGAAACCAATCTTAGATTTTAACCCGTTACATTTCTTTGAAGCTCATAGTTCTCGAAGTTTGGCA
131 AGAAACCAATCTTAGATTTTAACCCGTTACATTTCTTTGAAGCTCATAGTTCTCGAAGTTTGGCA
65433005 CCCAGGCATCATTTCATATCGATATTCTAGTTCTCATTCCCACCCTCCAACACATGCCTAATTGG
196 CCCAGGCATCATTTCATATCGATATTCTAGTTCTCATTCCCACCCTCCAACACATGCCTAATTGG
65433070 AGCAATCCTTTCG
261 AGCAATCCTTTCG
65433083 CT
1 CT
65433085 GCCTAAATGC
Statistics
Matches: 529, Mismatches: 17, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
272 258 0.49
273 271 0.51
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.33
Consensus pattern (273 bp):
CTCCAAGCCTGTCGATCTTCATATAAATGACAAGAGAGAAGAATACTCATGACTTTTGTTGCCTC
TTCAATAGACATAAACTAGTAATTACATCCTCGTTCCACTTCCTCGAATTTTGATATATAAGTTC
AGAAACCAATCTTAGATTTTAACCCGTTACATTTCTTTGAAGCTCATAGTTCTCGAAGTTTGGCA
CCCAGGCATCATTTCATATCGATATTCTAGTTCTCATTCCCACCCTCCAACACATGCCTAATTGG
AGCAATCCTTTCG
Found at i:65438095 original size:20 final size:20
Alignment explanation
Indices: 65438070--65438111 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
65438060 AATTCTTTAT
65438070 TAAATTTAAATCTATTATAA
1 TAAATTTAAATCTATTATAA
65438090 TAAATTTAAATCTATTATAA
1 TAAATTTAAATCTATTATAA
65438110 TA
1 TA
65438112 TTTTTCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAATTTAAATCTATTATAA
Found at i:65446153 original size:23 final size:23
Alignment explanation
Indices: 65446127--65446174 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
65446117 ATCGGCTTTC
*
65446127 CTTGAGTAATTCCTTGCCTCCTA
1 CTTGAGTAATTCATTGCCTCCTA
65446150 CTTGAGTAATTCATTGCCTCCTA
1 CTTGAGTAATTCATTGCCTCCTA
65446173 CT
1 CT
65446175 CTCTGTATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.19, C:0.29, G:0.12, T:0.40
Consensus pattern (23 bp):
CTTGAGTAATTCATTGCCTCCTA
Found at i:65460109 original size:46 final size:45
Alignment explanation
Indices: 65460026--65460197 Score: 166
Period size: 46 Copynumber: 3.7 Consensus size: 45
65460016 CTAGTAGCTG
* * **
65460026 ATGCATGTCCCAAACATGTCTTACACTGGCT-TACATCTTGAGGCTG
1 ATGCATGTCCCAGACATGTCTTACACTAGCTCT-CATC-TGAGGCCA
* * **
65460072 ATGCATGTCCCAGACATGTCTTACACTAACTCTCATCTCACTACCA
1 ATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCTGA-GGCCA
* ** * *
65460118 ATGCCATGTCCCTGACATGTTCTTACACTAGCTCTTGTAATGTGGCCA
1 ATG-CATGTCCCAGACATG-TCTTACACTAGCTCTCAT-CTGAGGCCA
65460166 ATGCATGTCCCAGACATGTCTTACACTAGCTC
1 ATGCATGTCCCAGACATGTCTTACACTAGCTC
65460198 ACAATAGTCA
Statistics
Matches: 103, Mismatches: 18, Indels: 10
0.79 0.14 0.08
Matches are distributed among these distances:
45 2 0.02
46 50 0.49
47 29 0.28
48 21 0.20
49 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.16, T:0.30
Consensus pattern (45 bp):
ATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCTGAGGCCA
Found at i:65463545 original size:22 final size:21
Alignment explanation
Indices: 65463510--65463558 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
65463500 TGTATTTATA
* *
65463510 TATTTTTTATAATTTTCTATT
1 TATTTTTTAGAATTTTCAATT
65463531 TATTCTTTTAGAATTTTCAATT
1 TATT-TTTTAGAATTTTCAATT
65463553 TCATTT
1 T-ATTT
65463559 AAAAGAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 4 0.17
22 17 0.71
23 3 0.12
ACGTcount: A:0.24, C:0.08, G:0.02, T:0.65
Consensus pattern (21 bp):
TATTTTTTAGAATTTTCAATT
Found at i:65463581 original size:20 final size:21
Alignment explanation
Indices: 65463540--65463589 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
65463530 TTATTCTTTT
65463540 AGAATTTTCAATTTCATTTAAA
1 AGAATTTTCAATTT-ATTTAAA
*
65463562 AGAATTTTGAATTT-TTTAAA
1 AGAATTTTCAATTTATTTAAA
*
65463582 ATAATTTT
1 AGAATTTT
65463590 TATATAGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 13 0.50
22 13 0.50
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (21 bp):
AGAATTTTCAATTTATTTAAA
Found at i:65469805 original size:17 final size:17
Alignment explanation
Indices: 65469779--65469811 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
65469769 TAAAGAAAAT
*
65469779 TTAAAGCAACTTATAAA
1 TTAAAACAACTTATAAA
65469796 TTAAAACAACTTATAA
1 TTAAAACAACTTATAA
65469812 TTGGGAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.12, G:0.03, T:0.30
Consensus pattern (17 bp):
TTAAAACAACTTATAAA
Found at i:65471106 original size:3 final size:3
Alignment explanation
Indices: 65471098--65471125 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
65471088 AATCTAATTC
65471098 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
65471126 GATATCATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:65477246 original size:174 final size:174
Alignment explanation
Indices: 65476833--65477324 Score: 670
Period size: 174 Copynumber: 2.8 Consensus size: 174
65476823 ATTAAACTAC
* * * *
65476833 TATGATGAATTTGCA-TATTTGTTGCTGTGATGATTATATTAAAATTTATGAAAATTTTGTGAAT
1 TATG-TGAATATGCAGT-TTTGTTGCTGTGATGATTATATTAGAATTTATGAAAA-TTTATGAAA
* *
65476897 CATCGGCAACTATGTCGATCTGAGCGGTTACCTGAGCAACAAAATTTGTTCAAATTCTA-TCTCT
63 CATCGACAACTATGTCGATCTGAGCGGTTACCTGAGCAACAAAATTTGTTCAAATTC-AGTTTCT
* * * *
65476961 TTGTAGATTTATCACATTGTTTTAATCGTCTTACAATTAATCTTATTG
127 TTGTTGATTTATTACACTGCTTTAATCGTCTTACAATTAATCTTATTG
65477009 TATGTGAATATGCAGTTTTGTTGCTGTGATGATTATATTAGAATTTATGAAAAATTTATGAAACA
1 TATGTGAATATGCAGTTTTGTTGCTGTGATGATTATATTAGAATTTATG-AAAATTTATGAAACA
*
65477074 TCGACAACTATGTCGATCTGAGCGGTTACCTGAGCAACAAAATTTGTTCAAATTCAGTTTCCTTG
65 TCGACAACTATGTCGATCTGAGCGGTTACCTGAGCAACAAAATTTGTTCAAATTCAGTTTCTTTG
* * * ** *
65477139 TTGATTTATTACGCT-CTTTAGTTGTCTTATGA-TACATTTTATTG
130 TTGATTTATTACACTGCTTTAATCGTCTTACAATTA-ATCTTATTG
* *
65477183 TATGTGAATCTG-TGATTTTGTTGCTGTGATGATTATATTAGAATTTATGAAAATTTAATGAAAC
1 TATGTGAATATGCAG-TTTTGTTGCTGTGATGATTATATTAGAATTTATGAAAATTT-ATGAAAC
* * *
65477247 ATTGACAACCATGTCGATCTGAGCGGTTACATGAGCAACAAAATTTGTTCAAATTCAGTTTCTTT
64 ATCGACAACTATGTCGATCTGAGCGGTTACCTGAGCAACAAAATTTGTTCAAATTCAGTTTCTTT
*
65477312 CTTGATTTATTAC
129 GTTGATTTATTAC
65477325 TTTGGTTTAG
Statistics
Matches: 286, Mismatches: 24, Indels: 14
0.88 0.07 0.04
Matches are distributed among these distances:
173 10 0.03
174 146 0.51
175 121 0.42
176 9 0.03
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.41
Consensus pattern (174 bp):
TATGTGAATATGCAGTTTTGTTGCTGTGATGATTATATTAGAATTTATGAAAATTTATGAAACAT
CGACAACTATGTCGATCTGAGCGGTTACCTGAGCAACAAAATTTGTTCAAATTCAGTTTCTTTGT
TGATTTATTACACTGCTTTAATCGTCTTACAATTAATCTTATTG
Found at i:65480268 original size:16 final size:15
Alignment explanation
Indices: 65480242--65480276 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
65480232 TGATGTGAAT
65480242 AATATAAAATATTAA
1 AATATAAAATATTAA
*
65480257 AATATCAAAATATTAG
1 AATAT-AAAATATTAA
65480273 AATA
1 AATA
65480277 ATAATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (15 bp):
AATATAAAATATTAA
Found at i:65482029 original size:32 final size:32
Alignment explanation
Indices: 65481988--65482050 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
65481978 TAATATACAT
* *
65481988 ATATGGTAAGGTATTGAAACAAAATAGGAAAG
1 ATATGGTAAGGAATTGAAACAAAACAGGAAAG
65482020 ATATGGTAAGGAATTGAAACAAAACAGGAAA
1 ATATGGTAAGGAATTGAAACAAAACAGGAAA
65482051 CATAGGTGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.52, C:0.05, G:0.24, T:0.19
Consensus pattern (32 bp):
ATATGGTAAGGAATTGAAACAAAACAGGAAAG
Found at i:65483186 original size:23 final size:23
Alignment explanation
Indices: 65483160--65483203 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
65483150 TTTGGGCTTC
65483160 GGTGCTCCTATTACTT-GCACTTT
1 GGTGCTCCTATT-CTTGGCACTTT
*
65483183 GGTGCTTCTATTCTTGGCACT
1 GGTGCTCCTATTCTTGGCACT
65483204 ATCGTGTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.11, C:0.25, G:0.20, T:0.43
Consensus pattern (23 bp):
GGTGCTCCTATTCTTGGCACTTT
Found at i:65486364 original size:21 final size:21
Alignment explanation
Indices: 65486323--65486364 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
65486313 AATTAGTATC
* *
65486323 TAATTAATCTTAACTTTAACT
1 TAATTAATATTAACTTAAACT
65486344 TAATTAATTATTAA-TTAAACT
1 TAATTAA-TATTAACTTAAACT
65486365 AAAGACAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.48
Consensus pattern (21 bp):
TAATTAATATTAACTTAAACT
Found at i:65489320 original size:34 final size:35
Alignment explanation
Indices: 65489282--65489351 Score: 90
Period size: 34 Copynumber: 2.0 Consensus size: 35
65489272 AGTCCCTTCT
* *
65489282 AACATGCAATACAACTAA-TACAAACAGATA-ATCA
1 AACATGAAATACAA-AAACTACAAACAGATATATCA
*
65489316 AACATGAAATACAAAAACTGCAAACAGATATATCA
1 AACATGAAATACAAAAACTACAAACAGATATATCA
65489351 A
1 A
65489352 TTCCTTCCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 2 0.06
34 24 0.77
35 5 0.16
ACGTcount: A:0.57, C:0.19, G:0.07, T:0.17
Consensus pattern (35 bp):
AACATGAAATACAAAAACTACAAACAGATATATCA
Found at i:65490805 original size:12 final size:13
Alignment explanation
Indices: 65490788--65490817 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
65490778 TAACCAATGT
65490788 AAAATAATTAA-A
1 AAAATAATTAACA
65490800 AAAATAATTAACA
1 AAAATAATTAACA
65490813 AAAAT
1 AAAAT
65490818 CGCTCTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.23
Consensus pattern (13 bp):
AAAATAATTAACA
Found at i:65491341 original size:32 final size:32
Alignment explanation
Indices: 65491305--65491369 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 32
65491295 ATTAATATAC
65491305 ATATATGGTAA-GATATTGAAACAAAATAGGAA
1 ATATATGGTAAGGA-ATTGAAACAAAATAGGAA
65491337 ATATATGGTAAGGAATTGAAACAAAATAGGAA
1 ATATATGGTAAGGAATTGAAACAAAATAGGAA
65491369 A
1 A
65491370 CATAGGTGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 30 0.94
33 2 0.06
ACGTcount: A:0.54, C:0.03, G:0.20, T:0.23
Consensus pattern (32 bp):
ATATATGGTAAGGAATTGAAACAAAATAGGAA
Found at i:65492643 original size:22 final size:23
Alignment explanation
Indices: 65492601--65492645 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
65492591 TTTAGATAAA
65492601 ATAAAAAATTATTAATAATTTTC
1 ATAAAAAATTATTAATAATTTTC
* *
65492624 ATAAAATATTATT-ATTATTTTC
1 ATAAAAAATTATTAATAATTTTC
65492646 TTAATTTATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (23 bp):
ATAAAAAATTATTAATAATTTTC
Found at i:65495157 original size:112 final size:112
Alignment explanation
Indices: 65494969--65495190 Score: 358
Period size: 112 Copynumber: 2.0 Consensus size: 112
65494959 GACACATGGT
*
65494969 CGTGTCTCTACCCGTGTGTTTACTACCTTGCATACTGACTTGTAAAATTTATGTGCATGGGACAC
1 CGTGTCTCTACCCGTGTGTTTACTACCTTGCATACTGACTTGTAAAATTTACGTGCATGGGACAC
65495034 ACAGCCGGACAACATGCCCATAGGGCTGGCCATGTGTCACACACGAC
66 ACAGCCGGACAACATGCCCATAGGGCTGGCCATGTGTCACACACGAC
*
65495081 CGTGTCTCTACCCGTGTGTTTACTACCATT-CATATTGACTTGTAAAATTTACGTGCA-GGAGAC
1 CGTGTCTCTACCCGTGTGTTTACTACC-TTGCATACTGACTTGTAAAATTTACGTGCATGG-GAC
* ** *
65495144 ACACGGCCGGACAACATGCTTATGGGGCTGGCCATGTGTCACACACG
64 ACACAGCCGGACAACATGCCCATAGGGCTGGCCATGTGTCACACACG
65495191 GCCTAGGCAT
Statistics
Matches: 102, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
111 2 0.02
112 98 0.96
113 2 0.02
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.27
Consensus pattern (112 bp):
CGTGTCTCTACCCGTGTGTTTACTACCTTGCATACTGACTTGTAAAATTTACGTGCATGGGACAC
ACAGCCGGACAACATGCCCATAGGGCTGGCCATGTGTCACACACGAC
Found at i:65497162 original size:63 final size:63
Alignment explanation
Indices: 65497063--65497944 Score: 1764
Period size: 63 Copynumber: 14.0 Consensus size: 63
65497053 TATTTCTTTT
65497063 TAGTCAAACAAGTCACCAAATTATTACCTAACATTGACTAGCCTAATTCTTTGTCCCTATGGC
1 TAGTCAAACAAGTCACCAAATTATTACCTAACATTGACTAGCCTAATTCTTTGTCCCTATGGC
65497126 TAGTCAAACAAGTCACCAAATTATTACCTAACATTGACTAGCCTAATTCTTTGTCCCTATGGC
1 TAGTCAAACAAGTCACCAAATTATTACCTAACATTGACTAGCCTAATTCTTTGTCCCTATGGC
65497189 TAGTCAAACAAGTCACCAAATTATTACCTAACATTGACTAGCCTAATTCTTTGTCCCTATGGC
1 TAGTCAAACAAGTCACCAAATTATTACCTAACATTGACTAGCCTAATTCTTTGTCCCTATGGC
65497252 TAGTCAAACAAGTCACCAAATTATTACCTAACATTGACTAGCCTAATTCTTTGTCCCTATGGC
1 TAGTCAAACAAGTCACCAAATTATTACCTAACATTGACTAGCCTAATTCTTTGTCCCTATGGC
65497315 TAGTCAAACAAGTCACCAAATTATTACCTAACATTGACTAGCCTAATTCTTTGTCCCTATGGC
1 TAGTCAAACAAGTCACCAAATTATTACCTAACATTGACTAGCCTAATTCTTTGTCCCTATGGC
65497378 TAGTCAAACAAGTCACCAAATTATTACCTAACATTGACTAGCCTAATTCTTTGTCCCTATGGC
1 TAGTCAAACAAGTCACCAAATTATTACCTAACATTGACTAGCCTAATTCTTTGTCCCTATGGC
65497441 TAGTCAAACAAGTCACCAAATTATTACCTAACATTGACTAGCCTAATTCTTTGTCCCTATGGC
1 TAGTCAAACAAGTCACCAAATTATTACCTAACATTGACTAGCCTAATTCTTTGTCCCTATGGC
65497504 TAGTCAAACAAGTCACCAAATTATTACCTAACATTGACTAGCCTAATTCTTTGTCCCTATGGC
1 TAGTCAAACAAGTCACCAAATTATTACCTAACATTGACTAGCCTAATTCTTTGTCCCTATGGC
65497567 TAGTCAAACAAGTCACCAAATTATTACCTAACATTGACTAGCCTAATTCTTTGTCCCTATGGC
1 TAGTCAAACAAGTCACCAAATTATTACCTAACATTGACTAGCCTAATTCTTTGTCCCTATGGC
65497630 TAGTCAAACAAGTCACCAAATTATTACCTAACATTGACTAGCCTAATTCTTTGTCCCTATGGC
1 TAGTCAAACAAGTCACCAAATTATTACCTAACATTGACTAGCCTAATTCTTTGTCCCTATGGC
65497693 TAGTCAAACAAGTCACCAAATTATTACCTAACATTGACTAGCCTAATTCTTTGTCCCTATGGC
1 TAGTCAAACAAGTCACCAAATTATTACCTAACATTGACTAGCCTAATTCTTTGTCCCTATGGC
65497756 TAGTCAAACAAGTCACCAAATTATTACCTAACATTGACTAGCCTAATTCTTTGTCCCTATGGC
1 TAGTCAAACAAGTCACCAAATTATTACCTAACATTGACTAGCCTAATTCTTTGTCCCTATGGC
65497819 TAGTCAAACAAGTCACCAAATTATTACCTAACATTGACTAGCCTAATTCTTTGTCCCTATGGC
1 TAGTCAAACAAGTCACCAAATTATTACCTAACATTGACTAGCCTAATTCTTTGTCCCTATGGC
65497882 TAGTCAAACAAGTCACCAAATTATTACCTAACATTGACTAGCCTAATTCTTTGTCCCTATGGC
1 TAGTCAAACAAGTCACCAAATTATTACCTAACATTGACTAGCCTAATTCTTTGTCCCTATGGC
65497945 CAGCCATGTT
Statistics
Matches: 819, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 819 1.00
ACGTcount: A:0.32, C:0.25, G:0.11, T:0.32
Consensus pattern (63 bp):
TAGTCAAACAAGTCACCAAATTATTACCTAACATTGACTAGCCTAATTCTTTGTCCCTATGGC
Found at i:65503309 original size:21 final size:21
Alignment explanation
Indices: 65503255--65503310 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
65503245 CTTTGAAATA
* *
65503255 GGGC-ACACGCCCATGTGGAT
1 GGGCAACACGCCCGTATGGAT
* * *
65503275 AGGAAACACTCCCGTATGGAT
1 GGGCAACACGCCCGTATGGAT
65503296 GGGCAACACGCCCGT
1 GGGCAACACGCCCGT
65503311 GCGAAACTTG
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.25, C:0.30, G:0.30, T:0.14
Consensus pattern (21 bp):
GGGCAACACGCCCGTATGGAT
Found at i:65508663 original size:45 final size:45
Alignment explanation
Indices: 65508602--65508759 Score: 235
Period size: 45 Copynumber: 3.5 Consensus size: 45
65508592 TAAGATTGAG
*
65508602 ATATGTGTTTTCGTGTAAGACCACGTCAGGGACGTTGGCATCGAT
1 ATATGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGAT
* *
65508647 ATATGTGTTTTTGTGTAAGACCACGCCTGGGACGTTGGCATCGAT
1 ATATGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGAT
* * *
65508692 ATATGTGTTTTCGTGTAAGACCACCTCTGGAACATTGGCATCGAT
1 ATATGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGAT
* * *
65508737 CTATGTGGTTACGTGTAAGACCA
1 ATATGTGTTTTCGTGTAAGACCA
65508760 TTTTTGGGAC
Statistics
Matches: 102, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 102 1.00
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (45 bp):
ATATGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGAT
Found at i:65508778 original size:45 final size:45
Alignment explanation
Indices: 65508602--65508779 Score: 124
Period size: 45 Copynumber: 4.0 Consensus size: 45
65508592 TAAGATTGAG
* * * * * * **
65508602 ATATGTGTTTTCGTGTAAGACCACGTCAGGGACGTTGGCATCGAT
1 ATATGTGGTTACGTGTAAGACCACCTCTGGAACATCAGCATCGAT
* ** * * **
65508647 ATATGTGTTTTTGTGTAAGACCACGC-CTGGGACGTTGGCATCGAT
1 ATATGTGGTTACGTGTAAGACCAC-CTCTGGAACATCAGCATCGAT
* * **
65508692 ATATGTGTTTTCGTGTAAGACCACCTCTGGAACATTGGCATCGAT
1 ATATGTGGTTACGTGTAAGACCACCTCTGGAACATCAGCATCGAT
* ** * *
65508737 CTATGTGGTTACGTGTAAGACCATTTTTGGGACATCAGCATCG
1 ATATGTGGTTACGTGTAAGACCACCTCTGGAACATCAGCATCG
65508780 TATTTGATTC
Statistics
Matches: 116, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
44 1 0.01
45 115 0.99
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (45 bp):
ATATGTGGTTACGTGTAAGACCACCTCTGGAACATCAGCATCGAT
Found at i:65508778 original size:90 final size:90
Alignment explanation
Indices: 65508602--65508779 Score: 221
Period size: 90 Copynumber: 2.0 Consensus size: 90
65508592 TAAGATTGAG
* * * * **
65508602 ATATGTGTTTTCGTGTAAGACCACGTCAGGGACGTTGGCATCGATATATGTGTTTTTGTGTAAGA
1 ATATGTGTTTTCGTGTAAGACCACCTCAGGAACATTGGCATCGATATATGTGGTTACGTGTAAGA
* **
65508667 CCACGCCTGGGACGTTGGCATCGAT
66 CCACGCCTGGGACATCAGCATCGAT
* *
65508692 ATATGTGTTTTCGTGTAAGACCACCTCTGGAACATTGGCATCGATCTATGTGGTTACGTGTAAGA
1 ATATGTGTTTTCGTGTAAGACCACCTCAGGAACATTGGCATCGATATATGTGGTTACGTGTAAGA
****
65508757 CCATTTTTGGGACATCAGCATCG
66 CCACGCCTGGGACATCAGCATCG
65508780 TATTTGATTC
Statistics
Matches: 73, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
90 73 1.00
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (90 bp):
ATATGTGTTTTCGTGTAAGACCACCTCAGGAACATTGGCATCGATATATGTGGTTACGTGTAAGA
CCACGCCTGGGACATCAGCATCGAT
Found at i:65513898 original size:48 final size:47
Alignment explanation
Indices: 65513778--65513989 Score: 202
Period size: 48 Copynumber: 4.5 Consensus size: 47
65513768 TATGTGTGGT
* * *
65513778 AGTGTAAGACATGTCTGGGACATGCATCAGCCAT--AG-CATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCC-TCGAGATATTA-AGCC
*
65513824 AGTGTAAGACATGTCTGGGACCTGCATCGGCCTCGAGATATTTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATA-TTAAGCC
* * * *
65513872 AGTGTAAGACATGTCTAGGACATGCATCGGCATTGAGATGA-T-AGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGAT-ATTAAGCC
* * * *
65513918 AGTGTAAGACATGTCTGGGACATGTATCGGCC-CCACGATATACAAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGA-GATAT-TAAGCC
* *
65513966 AGTGTAAGACGTATCTGGGACATG
1 AGTGTAAGACATGTCTGGGACATG
65513990 GCGTTAGCTT
Statistics
Matches: 140, Mismatches: 17, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
45 3 0.02
46 65 0.46
47 3 0.02
48 66 0.47
49 3 0.02
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.24
Consensus pattern (47 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATTAAGCC
Found at i:65513927 original size:94 final size:95
Alignment explanation
Indices: 65513778--65514093 Score: 315
Period size: 94 Copynumber: 3.4 Consensus size: 95
65513768 TATGTGTGGT
* *
65513778 AGTGTAAGACATGTCTGGGACAT-GCATCAGCCA-T-AGCATGAGAGCCAGTGTAAGACATGTCT
1 AGTGTAAGACATGTCTGGGACATGGCATCAG-CATTGAG-ATGATAGCTAGTGTAAGACATGTCT
* **
65513840 GGGACCTGCATCGGCCTCGAGATATTTAAGCC
64 GGGACATGCATCGGCCTCGAGATATAAAAGCC
* *
65513872 AGTGTAAGACATGTCTAGGACAT-GCATCGGCATTGAGATGATAGCTAGTGTAAGACATGTCTGG
1 AGTGTAAGACATGTCTGGGACATGGCATCAGCATTGAGATGATAGCTAGTGTAAGACATGTCTGG
* * * *
65513936 GACATGTATCGGCC-CCACGATATACAAGCT
66 GACATGCATCGGCCTCGA-GATATAAAAGCC
* * * * * * * *
65513966 AGTGTAAGACGTATCTGGGACATGGCGTTAGC-TTGTGGTG-T-GTTAGTGTAAGACCTGTCTGG
1 AGTGTAAGACATGTCTGGGACATGGCATCAGCATTGAGATGATAGCTAGTGTAAGACATGTCTGG
* ** * *
65514028 GACATGGCATCAGCCTCGCTACATGAAAGCC
66 GACAT-GCATCGGCCTCGAGATATAAAAGCC
65514059 AGTGTAAGACCATGTCTGGGACATGGCATCAGCAT
1 AGTGTAAGA-CATGTCTGGGACATGGCATCAGCAT
65514094 CTTAACCCAT
Statistics
Matches: 181, Mismatches: 33, Indels: 15
0.79 0.14 0.07
Matches are distributed among these distances:
92 24 0.13
93 28 0.15
94 121 0.67
95 8 0.04
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.24
Consensus pattern (95 bp):
AGTGTAAGACATGTCTGGGACATGGCATCAGCATTGAGATGATAGCTAGTGTAAGACATGTCTGG
GACATGCATCGGCCTCGAGATATAAAAGCC
Found at i:65513947 original size:46 final size:46
Alignment explanation
Indices: 65513778--65513948 Score: 204
Period size: 46 Copynumber: 3.7 Consensus size: 46
65513768 TATGTGTGGT
* *
65513778 AGTGTAAGACATGTCTGGGACATGCATCAGCCA-T-AGCATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATC-GGCATTGAG-ATGATAGCC
* * *
65513824 AGTGTAAGACATGTCTGGGACCTGCATCGGCCTCGAGAT-ATTTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGATGA--T-AGCC
* *
65513872 AGTGTAAGACATGTCTAGGACATGCATCGGCATTGAGATGATAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGATGATAGCC
*
65513918 AGTGTAAGACATGTCTGGGACATGTATCGGC
1 AGTGTAAGACATGTCTGGGACATGCATCGGC
65513949 CCCACGATAT
Statistics
Matches: 107, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
45 3 0.03
46 61 0.57
47 3 0.03
48 39 0.36
49 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGATGATAGCC
Found at i:65520122 original size:11 final size:11
Alignment explanation
Indices: 65520106--65520159 Score: 63
Period size: 12 Copynumber: 4.7 Consensus size: 11
65520096 TCAAAAATAA
*
65520106 ATAAAAGAAAG
1 ATAAAATAAAG
*
65520117 ATAAAATAAAA
1 ATAAAATAAAG
65520128 ATAAAAATAAAG
1 AT-AAAATAAAG
*
65520140 ATAAAAATAAAA
1 AT-AAAATAAAG
65520152 ATAAAATA
1 ATAAAATA
65520160 GATGGACTCA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
11 17 0.45
12 21 0.55
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.17
Consensus pattern (11 bp):
ATAAAATAAAG
Found at i:65520130 original size:6 final size:6
Alignment explanation
Indices: 65520119--65520157 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
65520109 AAAGAAAGAT
*
65520119 AAAATA AAAATA AAAATA AAGATA AAAATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAA
65520158 TAGATGGACT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:65520145 original size:18 final size:17
Alignment explanation
Indices: 65520098--65520159 Score: 83
Period size: 18 Copynumber: 3.7 Consensus size: 17
65520088 ATAAGTCTTC
*
65520098 AAAAAT-AAAT-AAAAG
1 AAAAATAAAATAAAAAT
*
65520113 AAAGATAAAATAAAAAT
1 AAAAATAAAATAAAAAT
65520130 AAAAATAAAGATAAAAAT
1 AAAAATAAA-ATAAAAAT
65520148 AAAAATAAAATA
1 AAAAATAAAATA
65520160 GATGGACTCA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
15 5 0.12
16 4 0.10
17 15 0.37
18 17 0.41
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (17 bp):
AAAAATAAAATAAAAAT
Found at i:65520158 original size:23 final size:22
Alignment explanation
Indices: 65520104--65520159 Score: 85
Period size: 23 Copynumber: 2.5 Consensus size: 22
65520094 CTTCAAAAAT
*
65520104 AAATAAAAGAAAGATAAAATAA
1 AAATAAAATAAAGATAAAATAA
65520126 AAATAAAAATAAAGATAAAAATAA
1 AAAT-AAAATAAAGAT-AAAATAA
65520150 AAATAAAATA
1 AAATAAAATA
65520160 GATGGACTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
22 4 0.13
23 16 0.52
24 11 0.35
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (22 bp):
AAATAAAATAAAGATAAAATAA
Found at i:65522113 original size:13 final size:13
Alignment explanation
Indices: 65522095--65522119 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
65522085 CAACATGGCC
65522095 ATGTCACACGCCT
1 ATGTCACACGCCT
65522108 ATGTCACACGCC
1 ATGTCACACGCC
65522120 CGTTTGGGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.40, G:0.16, T:0.20
Consensus pattern (13 bp):
ATGTCACACGCCT
Found at i:65532514 original size:16 final size:16
Alignment explanation
Indices: 65532493--65532530 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
65532483 TTTTTGGCTG
*
65532493 GTATAGCGTGGATGGT
1 GTATAGCGTGAATGGT
*
65532509 GTATAGGGTGAATGGT
1 GTATAGCGTGAATGGT
65532525 GTATAG
1 GTATAG
65532531 ACTAATCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.24, C:0.03, G:0.42, T:0.32
Consensus pattern (16 bp):
GTATAGCGTGAATGGT
Found at i:65533033 original size:258 final size:258
Alignment explanation
Indices: 65532576--65533091 Score: 980
Period size: 258 Copynumber: 2.0 Consensus size: 258
65532566 AATTGCAATG
65532576 GGAAAATCATATGTTTAAATGATCAAATTGTCCTTTTAGTCTTATGTTTATTGTCACTGCATTAT
1 GGAAAATCATATGTTTAAATGATCAAATTGTCCTTTTAGTCTTATGTTTATTGTCACTGCATTAT
65532641 TTATTAAGCTAAATTAAATTAGGCTTAAACAACAAATATTGGTCATTACTTCCAAGCATAATGTT
66 TTATTAAGCTAAATTAAATTAGGCTTAAACAACAAATATTGGTCATTACTTCCAAGCATAATGTT
* *
65532706 AAATTACATAAAAAAATAATAAATATTTGTCAATCAACATTTGCAACTGCTAGCTGCATACATTT
131 AAATTACATAAAAAAACAACAAATATTTGTCAATCAACATTTGCAACTGCTAGCTGCATACATTT
65532771 ATCCAAATTGCAATAGGGAAATCATATGCTTAAATGATCAAATTTGTCCTTTTAATCTTATCT
196 ATCCAAATTGCAATAGGGAAATCATATGCTTAAATGATCAAATTTGTCCTTTTAATCTTATCT
65532834 GGAAAATCATATGTTTAAATGATCAAATTGTCCTTTTAGTCTTATGTTTATTGTCACTGCATTAT
1 GGAAAATCATATGTTTAAATGATCAAATTGTCCTTTTAGTCTTATGTTTATTGTCACTGCATTAT
65532899 TTATTAAGCTAAATTAAATTAGGCTTAAACAACAAATATTGGTCATTACTTCCAAGCATAATGTT
66 TTATTAAGCTAAATTAAATTAGGCTTAAACAACAAATATTGGTCATTACTTCCAAGCATAATGTT
* *
65532964 AAATTACATAAAAAAACAACCAATA-TTGCTCAATGAACATTTGCAACTGCTAGCTGCATACATT
131 AAATTACATAAAAAAACAACAAATATTTG-TCAATCAACATTTGCAACTGCTAGCTGCATACATT
65533028 TATCCAAATTGCAATAGGGAAATCATATGCTTAAATGATCAAATTTGTCCTTTTAATCTTATCT
195 TATCCAAATTGCAATAGGGAAATCATATGCTTAAATGATCAAATTTGTCCTTTTAATCTTATCT
65533092 TTATTGTCAC
Statistics
Matches: 253, Mismatches: 4, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
257 3 0.01
258 250 0.99
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (258 bp):
GGAAAATCATATGTTTAAATGATCAAATTGTCCTTTTAGTCTTATGTTTATTGTCACTGCATTAT
TTATTAAGCTAAATTAAATTAGGCTTAAACAACAAATATTGGTCATTACTTCCAAGCATAATGTT
AAATTACATAAAAAAACAACAAATATTTGTCAATCAACATTTGCAACTGCTAGCTGCATACATTT
ATCCAAATTGCAATAGGGAAATCATATGCTTAAATGATCAAATTTGTCCTTTTAATCTTATCT
Found at i:65533104 original size:211 final size:210
Alignment explanation
Indices: 65532837--65533234 Score: 672
Period size: 211 Copynumber: 1.9 Consensus size: 210
65532827 CTTATCTGGA
* * *
65532837 AAATCATATGTTTAAATGATCAAATTGTCCTTTTAGTCTTATGTTTATTGTCACTGCATTATTTA
1 AAATCATATGCTTAAATGATCAAATTGTCCTTTTAATCTTATCTTTATTGTCACTGCATTATTTA
* * * *
65532902 TTAAGCTAAATTAAATTAGGCTTAAACAACAAATATTGGTCATTACTTCCAAGCATAATGTTAAA
66 CTAAGCTAAATTAAATTAGGCATAAACAAAAAATATTGGTCATTACTGCCAAGCATAATGTTAAA
* *
65532967 TTACATAAAAAAACAACCAATA-TTGCTCAATGAACATTTGCAACTGCTAGCTGCATACATTTAT
131 TTACATAAAAAAACAACAAATATTTG-TCAATCAACATTTGCAACTGCTAGCTGCATACATTTAT
65533031 CCAAATTGCAATAGGG
195 CCAAATTGCAATAGGG
65533047 AAATCATATGCTTAAATGATCAAATTTGTCCTTTTAATCTTATCTTTATTGTCACTGCATTATTT
1 AAATCATATGCTTAAATGATCAAA-TTGTCCTTTTAATCTTATCTTTATTGTCACTGCATTATTT
65533112 ACTAAGCTAAATTAAATTAGGCATAAACAAAAAATATTGGTCATTACTGCCAAGCATAATGTTAA
65 ACTAAGCTAAATTAAATTAGGCATAAACAAAAAATATTGGTCATTACTGCCAAGCATAATGTTAA
* *
65533177 ATTACATAAAAAAATAATAAATATTTGTCAATCAACATTTGCAACTGCTAGCTGCATA
130 ATTACATAAAAAAACAACAAATATTTGTCAATCAACATTTGCAACTGCTAGCTGCATA
65533235 TGCCTCTTAC
Statistics
Matches: 175, Mismatches: 11, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
210 23 0.13
211 149 0.85
212 3 0.02
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (210 bp):
AAATCATATGCTTAAATGATCAAATTGTCCTTTTAATCTTATCTTTATTGTCACTGCATTATTTA
CTAAGCTAAATTAAATTAGGCATAAACAAAAAATATTGGTCATTACTGCCAAGCATAATGTTAAA
TTACATAAAAAAACAACAAATATTTGTCAATCAACATTTGCAACTGCTAGCTGCATACATTTATC
CAAATTGCAATAGGG
Found at i:65534397 original size:17 final size:16
Alignment explanation
Indices: 65534357--65534404 Score: 69
Period size: 16 Copynumber: 2.9 Consensus size: 16
65534347 GAATGCTAAT
*
65534357 GATTTAGGGATTTCAA
1 GATTTAGGGATTTAAA
65534373 GATTTAGGGATTTAAA
1 GATTTAGGGATTTAAA
*
65534389 GATTTTAGGTATTTAA
1 GA-TTTAGGGATTTAA
65534405 TGAAGATTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 17 0.59
17 12 0.41
ACGTcount: A:0.33, C:0.02, G:0.23, T:0.42
Consensus pattern (16 bp):
GATTTAGGGATTTAAA
Found at i:65541016 original size:6 final size:6
Alignment explanation
Indices: 65541005--65541039 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
65540995 AAGACAATGT
65541005 TTATCC TTATCC TTATCC TTATCC TTATCC TTATC
1 TTATCC TTATCC TTATCC TTATCC TTATCC TTATC
65541040 TTTTGAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.17, C:0.31, G:0.00, T:0.51
Consensus pattern (6 bp):
TTATCC
Found at i:65546366 original size:33 final size:33
Alignment explanation
Indices: 65546327--65546418 Score: 107
Period size: 33 Copynumber: 2.8 Consensus size: 33
65546317 GATGTGTATA
65546327 TTCCTTTCCAAGTGGTACACACAAAGTATACCT
1 TTCCTTTCCAAGTGGTACACACAAAGTATACCT
* *
65546360 TTCCTTTTCATA-TGGTATACACAAAGTATACCT
1 TTCCTTTCCA-AGTGGTACACACAAAGTATACCT
** * *
65546393 AACCTTTCCAAGT-ATAGACACAAAGT
1 TTCCTTTCCAAGTGGTACACACAAAGT
65546419 GTACATAACA
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
32 12 0.24
33 37 0.74
34 1 0.02
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.32
Consensus pattern (33 bp):
TTCCTTTCCAAGTGGTACACACAAAGTATACCT
Found at i:65547187 original size:47 final size:47
Alignment explanation
Indices: 65547133--65547233 Score: 118
Period size: 46 Copynumber: 2.2 Consensus size: 47
65547123 ATAATCTTTC
*
65547133 ATTTTCTATCAAAAACT-TTCAATTTACAGTATATTCATCCATGGGCA
1 ATTTTCTAT-AAAAACTGTTCAATTTACAGCATATTCATCCATGGGCA
*** *
65547180 ATTTTC--TAAACTTTGGTTCAATTTACAGCATATTCATCCATGGGTA
1 ATTTTCTATAAAAACT-GTTCAATTTACAGCATATTCATCCATGGGCA
65547226 ATTTTCTA
1 ATTTTCTA
65547234 AACTTTGGTT
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
44 4 0.09
45 1 0.02
46 34 0.76
47 6 0.13
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.42
Consensus pattern (47 bp):
ATTTTCTATAAAAACTGTTCAATTTACAGCATATTCATCCATGGGCA
Found at i:65547203 original size:46 final size:46
Alignment explanation
Indices: 65547150--65547243 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
65547140 ATCAAAAACT
*
65547150 TTCAATTTACAGTATATTCATCCATGGGCAATTTTCTAAACTTTGG
1 TTCAATTTACAGCATATTCATCCATGGGCAATTTTCTAAACTTTGG
*
65547196 TTCAATTTACAGCATATTCATCCATGGGTAATTTTCTAAACTTTGG
1 TTCAATTTACAGCATATTCATCCATGGGCAATTTTCTAAACTTTGG
65547242 TT
1 TT
65547244 TTCTTTTAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.43
Consensus pattern (46 bp):
TTCAATTTACAGCATATTCATCCATGGGCAATTTTCTAAACTTTGG
Found at i:65547932 original size:47 final size:45
Alignment explanation
Indices: 65547881--65547972 Score: 157
Period size: 47 Copynumber: 2.0 Consensus size: 45
65547871 GCTACCGGAG
65547881 GGAAGGTCTCATCGTATAGATGTCTTCTTTCTGTGTGTAGTCTTT
1 GGAAGGTCTCATCGTATAGATGTCTTCTTTCTGTGTGTAGTCTTT
*
65547926 NNGGAAGGTCTCATCGTATAGATGTCTTCTTTCTGTGTGTATTCTTT
1 --GGAAGGTCTCATCGTATAGATGTCTTCTTTCTGTGTGTAGTCTTT
65547973 CCCTACAAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.15, C:0.15, G:0.23, T:0.45
Consensus pattern (45 bp):
GGAAGGTCTCATCGTATAGATGTCTTCTTTCTGTGTGTAGTCTTT
Found at i:65557814 original size:5 final size:5
Alignment explanation
Indices: 65557804--65557828 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
65557794 TCAAAGTCAG
65557804 CTTTT CTTTT CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT
65557829 TTCAGAGCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
CTTTT
Found at i:65566669 original size:27 final size:27
Alignment explanation
Indices: 65566629--65566680 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
65566619 ACTTTGTAAA
65566629 TTGATTAAATTAATTAGTTATTGTATTT
1 TTGATTAAATTAATTAGTTA-TGTATTT
* *
65566657 TTGATTTAA-TAATTATTTATGTAT
1 TTGATTAAATTAATTAGTTATGTAT
65566681 GTTGTGGTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 5 0.23
27 9 0.41
28 8 0.36
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.58
Consensus pattern (27 bp):
TTGATTAAATTAATTAGTTATGTATTT
Found at i:65567190 original size:40 final size:40
Alignment explanation
Indices: 65567129--65567705 Score: 779
Period size: 40 Copynumber: 14.4 Consensus size: 40
65567119 TCGGGTGAAG
* *
65567129 AATAGATATATAAAATGGTTATATGAATTGATTATATGGA
1 AATAGATATATGAAATGGTTATATGAATCGATTATATGGA
* * *
65567169 AATAGATAAATGAAATAGTTATATGAATCGATTATATGAAA
1 AATAGATATATGAAATGGTTATATGAATCGATTATATG-GA
* *
65567210 AATAAATATATGAAATGGTTATATGAATCGATTATATGAAA
1 AATAGATATATGAAATGGTTATATGAATCGATTATATG-GA
*
65567251 AATACATATATGAAATGGTTATATGAATCGATTATATGGA
1 AATAGATATATGAAATGGTTATATGAATCGATTATATGGA
* * *
65567291 AATAGATAAATGAAATTGTTATATGAATCAATTATATGGA
1 AATAGATATATGAAATGGTTATATGAATCGATTATATGGA
* * *
65567331 AATAGATAAATGAAATGGTTATATGAACCGGTTATATGGA
1 AATAGATATATGAAATGGTTATATGAATCGATTATATGGA
* * * * *
65567371 AGTAGATACATAAAATGGTTATACGAATCGTTTATATGGA
1 AATAGATATATGAAATGGTTATATGAATCGATTATATGGA
* *
65567411 AATAAATAAATGAAATGGTTATATGAATC-AGTTATATGGA
1 AATAGATATATGAAATGGTTATATGAATCGA-TTATATGGA
* * *
65567451 AGTAGATATATGAAAT-G-AATATGAATC-AGTTATATGAA
1 AATAGATATATGAAATGGTTATATGAATCGA-TTATATGGA
*
65567489 AATAGATAAATGAAATGGTTATATGAATCGATTATAT-GA
1 AATAGATATATGAAATGGTTATATGAATCGATTATATGGA
*
65567528 AAGTAGATATATGAAATGGTTATATGAATCGGTTATATGGA
1 AA-TAGATATATGAAATGGTTATATGAATCGATTATATGGA
* *
65567569 AGTAGATATATGAAATGGTTATATGAATCGGTTATATGGA
1 AATAGATATATGAAATGGTTATATGAATCGATTATATGGA
* *
65567609 AATAGATATATGAAATGGTTGTATGAATCAATTATATGGA
1 AATAGATATATGAAATGGTTATATGAATCGATTATATGGA
*
65567649 AATAGATATATGAAATGGTTATATGAATC-AGTTATATAGA
1 AATAGATATATGAAATGGTTATATGAATCGA-TTATATGGA
65567689 AATAGATATATGAAATG
1 AATAGATATATGAAATG
65567706 AAACATTGGA
Statistics
Matches: 481, Mismatches: 48, Indels: 16
0.88 0.09 0.03
Matches are distributed among these distances:
38 33 0.07
39 6 0.01
40 362 0.75
41 80 0.17
ACGTcount: A:0.45, C:0.03, G:0.19, T:0.34
Consensus pattern (40 bp):
AATAGATATATGAAATGGTTATATGAATCGATTATATGGA
Found at i:65567356 original size:13 final size:13
Alignment explanation
Indices: 65567135--65567705 Score: 225
Period size: 13 Copynumber: 42.8 Consensus size: 13
65567125 GAAGAATAGA
*
65567135 TATATAAAATGGT
1 TATATGAAATGGT
* *
65567148 TATATGAATTGAT
1 TATATGAAATGGT
* *
65567161 TATATGGAAATAGA
1 TATAT-GAAATGGT
* *
65567175 TAAATGAAATAGT
1 TATATGAAATGGT
*
65567188 TATATG-AATCGAT
1 TATATGAAAT-GGT
***
65567201 TATATGAAAAATAAA
1 TATATG--AAATGGT
65567216 TATATGAAATGGT
1 TATATGAAATGGT
*
65567229 TATATG-AATCGAT
1 TATATGAAAT-GGT
***
65567242 TATATGAAAAATACA
1 TATATG--AAATGGT
65567257 TATATGAAATGGT
1 TATATGAAATGGT
*
65567270 TATATG-AATCGAT
1 TATATGAAAT-GGT
* *
65567283 TATATGGAAATAGA
1 TATAT-GAAATGGT
* *
65567297 TAAATGAAATTGT
1 TATATGAAATGGT
**
65567310 TATATG-AATCAAT
1 TATATGAAAT-GGT
* *
65567323 TATATGGAAATAGA
1 TATAT-GAAATGGT
*
65567337 TAAATGAAATGGT
1 TATATGAAATGGT
**
65567350 TATATGAACCGGT
1 TATATGAAATGGT
* * *
65567363 TATATGGAAGTAGA
1 TATAT-GAAATGGT
* *
65567377 TACATAAAATGGT
1 TATATGAAATGGT
* *
65567390 TATACG-AATCGTT
1 TATATGAAAT-GGT
***
65567403 TATATGGAAATAAA
1 TATAT-GAAATGGT
*
65567417 TAAATGAAATGGT
1 TATATGAAATGGT
*
65567430 TATATG-AATCAGT
1 TATATGAAAT-GGT
* * *
65567443 TATATGGAAGTAGA
1 TATAT-GAAATGGT
65567457 TATATGAAAT-G-
1 TATATGAAATGGT
* *
65567468 AATATG-AATCAGT
1 TATATGAAAT-GGT
* *
65567481 TATATGAAAATAGA
1 TATATG-AAATGGT
*
65567495 TAAATGAAATGGT
1 TATATGAAATGGT
*
65567508 TATATG-AATCGAT
1 TATATGAAAT-GGT
* *
65567521 TATATGAAAGTAGA
1 TATATGAAA-TGGT
65567535 TATATGAAATGGT
1 TATATGAAATGGT
65567548 TATATG-AATCGGT
1 TATATGAAAT-GGT
* * *
65567561 TATATGGAAGTAGA
1 TATAT-GAAATGGT
65567575 TATATGAAATGGT
1 TATATGAAATGGT
65567588 TATATG-AATCGGT
1 TATATGAAAT-GGT
* *
65567601 TATATGGAAATAGA
1 TATAT-GAAATGGT
65567615 TATATGAAATGGT
1 TATATGAAATGGT
* **
65567628 TGTATG-AATCAAT
1 TATATGAAAT-GGT
* *
65567641 TATATGGAAATAGA
1 TATAT-GAAATGGT
65567655 TATATGAAATGGT
1 TATATGAAATGGT
*
65567668 TATATG-AATCAGT
1 TATATGAAAT-GGT
* *
65567681 TATATAGAAATAGA
1 TATAT-GAAATGGT
65567695 TATATGAAATG
1 TATATGAAATG
65567706 AAACATTGGA
Statistics
Matches: 414, Mismatches: 102, Indels: 84
0.69 0.17 0.14
Matches are distributed among these distances:
10 3 0.01
11 5 0.01
12 35 0.08
13 239 0.58
14 87 0.21
15 39 0.09
16 6 0.01
ACGTcount: A:0.44, C:0.03, G:0.19, T:0.34
Consensus pattern (13 bp):
TATATGAAATGGT
Found at i:65571239 original size:36 final size:36
Alignment explanation
Indices: 65571189--65571281 Score: 123
Period size: 36 Copynumber: 2.6 Consensus size: 36
65571179 GTAAATCGAC
* * *
65571189 AATCCAACCAAAACACACCATATGCTCATAAGAGCT
1 AATCCATCCAAAACACACCAAATGCTCATAAAAGCT
* *
65571225 AATCCATCCTAAACATACCAAATGCTCATAAAAGCT
1 AATCCATCCAAAACACACCAAATGCTCATAAAAGCT
* *
65571261 AATCTATCCGAAACACACCAA
1 AATCCATCCAAAACACACCAA
65571282 TGGCTCCGAA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 49 1.00
ACGTcount: A:0.45, C:0.30, G:0.06, T:0.18
Consensus pattern (36 bp):
AATCCATCCAAAACACACCAAATGCTCATAAAAGCT
Found at i:65583629 original size:34 final size:37
Alignment explanation
Indices: 65583590--65583658 Score: 99
Period size: 36 Copynumber: 1.9 Consensus size: 37
65583580 GGAAAATATG
* *
65583590 ATTGAATGTG-AATG-ATTTTTATTTGAA-AATGAAA
1 ATTGAATGTGAAATGTATGTTTATTTAAATAATGAAA
65583624 ATTGAATGTGAAATGTATGTTTATTTAAATAATGA
1 ATTGAATGTGAAATGTATGTTTATTTAAATAATGA
65583659 GTCTGGTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
34 10 0.33
35 4 0.13
36 11 0.37
37 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.17, T:0.42
Consensus pattern (37 bp):
ATTGAATGTGAAATGTATGTTTATTTAAATAATGAAA
Found at i:65584537 original size:18 final size:18
Alignment explanation
Indices: 65584510--65584552 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
65584500 TGCATAAAAA
* *
65584510 GAAAGCAAATAAATAAAC
1 GAAAGAAAATAAACAAAC
*
65584528 GAAAGAAAATAAACAAAT
1 GAAAGAAAATAAACAAAC
65584546 GAAAGAA
1 GAAAGAA
65584553 GGGGGAAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.70, C:0.07, G:0.14, T:0.09
Consensus pattern (18 bp):
GAAAGAAAATAAACAAAC
Found at i:65593288 original size:27 final size:26
Alignment explanation
Indices: 65593253--65593364 Score: 125
Period size: 27 Copynumber: 4.2 Consensus size: 26
65593243 AGCATGGCTG
*
65593253 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGACAGAGCCA
*
65593279 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGACAGAGCCA
* *
65593307 CCAGAACAGAAATATATGACAGAGCCA
1 CCAGAACAGATA-ATGTGACAGAGCCA
* * *
65593334 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGACAGAGCCA
65593361 CCAG
1 CCAG
65593365 GACGCTTCCT
Statistics
Matches: 72, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
26 6 0.08
27 49 0.68
28 17 0.24
ACGTcount: A:0.39, C:0.23, G:0.22, T:0.15
Consensus pattern (26 bp):
CCAGAACAGATAATGTGACAGAGCCA
Found at i:65593312 original size:54 final size:54
Alignment explanation
Indices: 65593253--65593364 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
65593243 AGCATGGCTG
* * *
65593253 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGAAATATATGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* *
65593307 CCAGAACAGAAATATATGACAGAGCCACCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGAAATATATGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
65593361 CCAG
1 CCAG
65593365 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 34 0.65
55 18 0.35
ACGTcount: A:0.39, C:0.23, G:0.22, T:0.15
Consensus pattern (54 bp):
CCAGAACAGAAATATATGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:65595975 original size:16 final size:16
Alignment explanation
Indices: 65595954--65595985 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
65595944 TTTCTCTCTC
*
65595954 TAGGGTTAGGTTTTTT
1 TAGGGTTAGATTTTTT
65595970 TAGGGTTAGATTTTTT
1 TAGGGTTAGATTTTTT
65595986 ATTTTATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.28, T:0.56
Consensus pattern (16 bp):
TAGGGTTAGATTTTTT
Found at i:65595985 original size:15 final size:16
Alignment explanation
Indices: 65595954--65595986 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
65595944 TTTCTCTCTC
*
65595954 TAGGGTTAGGTTTTTT
1 TAGGGTTAGGATTTTT
65595970 TAGGGTTA-GATTTTT
1 TAGGGTTAGGATTTTT
65595985 TA
1 TA
65595987 TTTTATTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.18, C:0.00, G:0.27, T:0.55
Consensus pattern (16 bp):
TAGGGTTAGGATTTTT
Found at i:65604453 original size:46 final size:44
Alignment explanation
Indices: 65604349--65604456 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
65604339 TGTCTTTGAC
** * * *
65604349 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
65604393 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
65604439 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
65604457 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:65607689 original size:18 final size:18
Alignment explanation
Indices: 65607666--65607718 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
65607656 AATGAAAAAG
65607666 ATGAGAAATGAATATGAA
1 ATGAGAAATGAATATGAA
*
65607684 ATGAGAAATAAAATATGAA
1 ATGAGAAAT-GAATATGAA
65607703 ATGATGAAATG-ATATG
1 ATGA-GAAATGAATATG
65607719 TGAAACTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 14 0.45
19 12 0.39
20 5 0.16
ACGTcount: A:0.55, C:0.00, G:0.21, T:0.25
Consensus pattern (18 bp):
ATGAGAAATGAATATGAA
Found at i:65607700 original size:19 final size:18
Alignment explanation
Indices: 65607666--65607712 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 18
65607656 AATGAAAAAG
*
65607666 ATGAGAAATGAATATGAA
1 ATGAGAAATAAATATGAA
65607684 ATGAGAAATAAAATATGAA
1 ATGAGAAAT-AAATATGAA
65607703 ATGATGAAAT
1 ATGA-GAAAT
65607713 GATATGTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 9 0.35
19 12 0.46
20 5 0.19
ACGTcount: A:0.57, C:0.00, G:0.19, T:0.23
Consensus pattern (18 bp):
ATGAGAAATAAATATGAA
Found at i:65612870 original size:24 final size:24
Alignment explanation
Indices: 65612833--65612884 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
65612823 TTCCCCGGTA
*
65612833 GAAGTCAAAACCGAAAAAGGGTCT
1 GAAGTCAAAACCGAAAAAAGGTCT
* *
65612857 GAAGTCGAATCCGAAAAAAGGTCT
1 GAAGTCAAAACCGAAAAAAGGTCT
65612881 GAAG
1 GAAG
65612885 AACACGTCCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.44, C:0.15, G:0.27, T:0.13
Consensus pattern (24 bp):
GAAGTCAAAACCGAAAAAAGGTCT
Found at i:65612994 original size:48 final size:48
Alignment explanation
Indices: 65612927--65613110 Score: 280
Period size: 48 Copynumber: 3.8 Consensus size: 48
65612917 GCCATGGCCG
* * * * *
65612927 ATGAATCGAAAGCAATAAGTTCTGTTCCAAAATCTGTAGAGAAAGCCG
1 ATGAACCGAAAGCAGTAAGTTCTGTTCCGAAATCTGCAGAGAAAGCCA
65612975 ATGAACCGAAAGCAGTAAGTTCTGTTCCGAAATCTGCAGA-AGAAGCCA
1 ATGAACCGAAAGCAGTAAGTTCTGTTCCGAAATCTGCAGAGA-AAGCCA
* *
65613023 ATGAATCGAAAGCAGTAAGTTCTGTTCCGAAATCTGCAGAGGAAGCCA
1 ATGAACCGAAAGCAGTAAGTTCTGTTCCGAAATCTGCAGAGAAAGCCA
*
65613071 ATGAACCAAAAGCAGTAAGTTCTGTTCCGAAATCTGCAGA
1 ATGAACCGAAAGCAGTAAGTTCTGTTCCGAAATCTGCAGA
65613111 AGAAGGAAGC
Statistics
Matches: 125, Mismatches: 9, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
47 1 0.01
48 124 0.99
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.21
Consensus pattern (48 bp):
ATGAACCGAAAGCAGTAAGTTCTGTTCCGAAATCTGCAGAGAAAGCCA
Found at i:65613091 original size:96 final size:96
Alignment explanation
Indices: 65612927--65613115 Score: 324
Period size: 96 Copynumber: 2.0 Consensus size: 96
65612917 GCCATGGCCG
* * *
65612927 ATGAATCGAAAGCAATAAGTTCTGTTCCAAAATCTGTAGAGAAAGCCGATGAACCGAAAGCAGTA
1 ATGAATCGAAAGCAATAAGTTCTGTTCCAAAATCTGCAGAGAAAGCCAATGAACCAAAAGCAGTA
65612992 AGTTCTGTTCCGAAATCTGCAGAAGAAGCCA
66 AGTTCTGTTCCGAAATCTGCAGAAGAAGCCA
* * *
65613023 ATGAATCGAAAGCAGTAAGTTCTGTTCCGAAATCTGCAGAGGAAGCCAATGAACCAAAAGCAGTA
1 ATGAATCGAAAGCAATAAGTTCTGTTCCAAAATCTGCAGAGAAAGCCAATGAACCAAAAGCAGTA
65613088 AGTTCTGTTCCGAAATCTGCAGAAGAAG
66 AGTTCTGTTCCGAAATCTGCAGAAGAAG
65613116 GAAGCGTTAG
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
96 87 1.00
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.21
Consensus pattern (96 bp):
ATGAATCGAAAGCAATAAGTTCTGTTCCAAAATCTGCAGAGAAAGCCAATGAACCAAAAGCAGTA
AGTTCTGTTCCGAAATCTGCAGAAGAAGCCA
Found at i:65613519 original size:9 final size:9
Alignment explanation
Indices: 65613507--65613565 Score: 57
Period size: 9 Copynumber: 6.6 Consensus size: 9
65613497 CAATTCCAGC
65613507 AGAAGAGAA
1 AGAAGAGAA
*
65613516 AGAAGTGAA
1 AGAAGAGAA
*
65613525 GGAAGTA-AA
1 AGAAG-AGAA
*
65613534 AGAAGTGAA
1 AGAAGAGAA
*
65613543 ACAAGAGAA
1 AGAAGAGAA
*
65613552 AGAAAAGAA
1 AGAAGAGAA
65613561 AGAAG
1 AGAAG
65613566 TAGCTCTGGG
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.63, C:0.02, G:0.31, T:0.05
Consensus pattern (9 bp):
AGAAGAGAA
Found at i:65626795 original size:16 final size:18
Alignment explanation
Indices: 65626769--65626814 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 18
65626759 TTCTCTTTTA
65626769 TTTATTTATTATTTAA-TC
1 TTTA-TTATTATTTAATTC
65626787 -TTATTATTA-TTAATTC
1 TTTATTATTATTTAATTC
65626803 TTTATT-TTATTT
1 TTTATTATTATTT
65626815 TACTTTGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
15 4 0.16
16 11 0.44
17 10 0.40
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTATTATTATTTAATTC
Found at i:65626796 original size:23 final size:23
Alignment explanation
Indices: 65626762--65626806 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
65626752 TTTCCCATTC
*
65626762 TCTTTTATTTATTTATTATTTAA
1 TCTTTTATTTATTAATTATTTAA
*
65626785 TCTTATTA-TTATTAATTCTTTA
1 TCTT-TTATTTATTAATTATTTA
65626807 TTTTATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (23 bp):
TCTTTTATTTATTAATTATTTAA
Found at i:65639084 original size:16 final size:16
Alignment explanation
Indices: 65639063--65639094 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
65639053 TATGGACCAA
65639063 TTATACATATGCTCAT
1 TTATACATATGCTCAT
65639079 TTATACATATGCTCAT
1 TTATACATATGCTCAT
65639095 CATACAACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (16 bp):
TTATACATATGCTCAT
Found at i:65642576 original size:40 final size:40
Alignment explanation
Indices: 65642519--65642708 Score: 238
Period size: 40 Copynumber: 4.8 Consensus size: 40
65642509 ATTTGAATAC
* * * *
65642519 ATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATTTT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGATGA-TAT
*
65642559 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGATGATAT
*
65642599 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGATGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGATGATAT
* * * * *
65642639 ATCCAGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGATGATAT
* * *
65642679 ACCCGGGTTAAGACCCGAAGGCAATTGTGC
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGC
65642709 TTGTGGTTAT
Statistics
Matches: 134, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
40 131 0.98
41 3 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGATGATAT
Found at i:65642652 original size:80 final size:80
Alignment explanation
Indices: 65642519--65642728 Score: 271
Period size: 80 Copynumber: 2.6 Consensus size: 80
65642509 ATTTGAATAC
* * * * *
65642519 ATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATTATATCCAGGCTAAGACCCGAAGGCATT
*
65642584 TGTGCAAGTTGATAT
66 CGTGCAAGTTGATAT
65642599 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGATGA-TATATCCAGGCTAAGACCCGAAGGCAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGATTATATCCAGGCTAAGACCCGAAGGCAT
* *
65642663 TCGTGCGAGTTGCTAT
65 TCGTGCAAGTTGATAT
* * * ** *
65642679 ACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATATCC-GGCTAA
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATTATATCCAGGCTAA
65642729 AATTCCGAAG
Statistics
Matches: 114, Mismatches: 14, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
79 8 0.07
80 103 0.90
81 3 0.03
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (80 bp):
ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATTATATCCAGGCTAAGACCCGAAGGCATT
CGTGCAAGTTGATAT
Found at i:65644368 original size:47 final size:47
Alignment explanation
Indices: 65644299--65644393 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
65644289 ATATAAACAA
65644299 ATTAAATTATTAATTCATCACATTCTTCAATTTCAACCCGAAAACTT
1 ATTAAATTATTAATTCATCACATTCTTCAATTTCAACCCGAAAACTT
65644346 ATTAAATTATTAATTCATCACATTCTTCAATTTCAACCCGAAAACTT
1 ATTAAATTATTAATTCATCACATTCTTCAATTTCAACCCGAAAACTT
65644393 A
1 A
65644394 CTCTATGGCA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.39, C:0.21, G:0.02, T:0.38
Consensus pattern (47 bp):
ATTAAATTATTAATTCATCACATTCTTCAATTTCAACCCGAAAACTT
Found at i:65645473 original size:21 final size:19
Alignment explanation
Indices: 65645424--65645473 Score: 68
Period size: 18 Copynumber: 2.6 Consensus size: 19
65645414 TCTTCTATTT
65645424 CTTTC-TCTTCTTCAGCAA
1 CTTTCTTCTTCTTCAGCAA
65645442 CTTTCTT-TTCTTCAGCAA
1 CTTTCTTCTTCTTCAGCAA
65645460 CAATTTCTTCTTCT
1 C--TTTCTTCTTCT
65645474 GCAGTAGCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 17 0.61
19 1 0.04
20 6 0.21
21 4 0.14
ACGTcount: A:0.16, C:0.30, G:0.04, T:0.50
Consensus pattern (19 bp):
CTTTCTTCTTCTTCAGCAA
Found at i:65645838 original size:21 final size:19
Alignment explanation
Indices: 65645789--65645838 Score: 68
Period size: 18 Copynumber: 2.6 Consensus size: 19
65645779 TCTTCTATTT
65645789 CTTTC-TCTTCTTCAGCAA
1 CTTTCTTCTTCTTCAGCAA
65645807 CTTTCTT-TTCTTCAGCAA
1 CTTTCTTCTTCTTCAGCAA
65645825 CAATTTCTTCTTCT
1 C--TTTCTTCTTCT
65645839 GCAGTAGCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 17 0.61
19 1 0.04
20 6 0.21
21 4 0.14
ACGTcount: A:0.16, C:0.30, G:0.04, T:0.50
Consensus pattern (19 bp):
CTTTCTTCTTCTTCAGCAA
Found at i:65646029 original size:365 final size:365
Alignment explanation
Indices: 65645359--65647515 Score: 4091
Period size: 365 Copynumber: 5.9 Consensus size: 365
65645349 CTAGATTTTT
65645359 AATATTTACACCCACAGATTCTAGTGTGGTGACAATATTCACATCAGAATCTTTCTCTTCTATTT
1 AATATTTACACCCACAGATTCTAGTGTGGTGACAATATTCACATCAGAATCTTTCTCTTCTATTT
* *
65645424 CTTTCTCTTCTTCAGCAACTTTCTTTTCTTCAGCAACAATTTCTTCTTCTGCAGTAGCAGCTTCC
66 CTTTCTCTTCTTCAGCAACTTCCTTTTCTTCAGCAACAATTTCCTCTTCTGCAGTAGCAGCTTCC
65645489 TTGTCAACAATAGTGCCCTATTGATCAGCAAAAATATCATTTTGAACAAGCTATCAATCTTGTGT
131 TTGTCAACAATAGTGCCCTATTGATCAGCAAAAATATCATTTTGAACAAGCTATCAATCTTGTGT
65645554 AGACATTCCTCAAAGCCTATGGATTCTTCATCTTTGTCATTATCAGAGACTTGCACGATAGGAGG
196 AGACATTCCTCAAAGCCTATGGATTCTTCATCTTTGTCATTATCAGAGACTTGCACGATAGGAGG
*
65645619 AGATGCCACCAATCGGTCTCAATCTTTGAAGTCGTCATTTTTAAATGAATGCTTATAGTTTCAAA
261 AGATGCCACCAATCGGTCTCAATCTTTGAAGTCGTCATTTGTAAATGAATGCTTATAGTTTCAAA
65645684 TGATTGGTGGAAATACTGGGAAGTTCGGTATTATAGTTTC
326 TGATTGGTGGAAATACTGGGAAGTTCGGTATTATAGTTTC
*
65645724 AATATTTACACCCATAGATTCTAGTGTGGTGACAATATTCACATCAGAATCTTTCTCTTCTATTT
1 AATATTTACACCCACAGATTCTAGTGTGGTGACAATATTCACATCAGAATCTTTCTCTTCTATTT
* *
65645789 CTTTCTCTTCTTCAGCAACTTTCTTTTCTTCAGCAACAATTTCTTCTTCTGCAGTAGCAGCTTCC
66 CTTTCTCTTCTTCAGCAACTTCCTTTTCTTCAGCAACAATTTCCTCTTCTGCAGTAGCAGCTTCC
65645854 TTGTCAACAATAGTGCCCTATTGATCAGCAAAAATATCATTTTGAACAAGCTATCAATCTTGTGT
131 TTGTCAACAATAGTGCCCTATTGATCAGCAAAAATATCATTTTGAACAAGCTATCAATCTTGTGT
65645919 AGACATTCCTCAAAGCCTATGGATTCTTCATCTTTGTCATTATCAGAGACTTGCACGATAGGAGG
196 AGACATTCCTCAAAGCCTATGGATTCTTCATCTTTGTCATTATCAGAGACTTGCACGATAGGAGG
*
65645984 AGATGCCACCAATCGGTCTCAATCTTTGAAGTCGTCATTTTTAAATGAATGCTTATAGTTTCAAA
261 AGATGCCACCAATCGGTCTCAATCTTTGAAGTCGTCATTTGTAAATGAATGCTTATAGTTTCAAA
65646049 TGATTGGTGGAAATACTGGGAAGTTCGGTATTATAGTTTC
326 TGATTGGTGGAAATACTGGGAAGTTCGGTATTATAGTTTC
*
65646089 AATATTTACACCCATAGATTCTAGTGTGGTGACAATATTCACATCAGAATCTTTCTCTTCTATTT
1 AATATTTACACCCACAGATTCTAGTGTGGTGACAATATTCACATCAGAATCTTTCTCTTCTATTT
65646154 CTTTCTCTTCTTCAGCAACTTCCTTTTCTTCAGCAACAATTTCCTCTTCTGCAGTAGCAGCTTCC
66 CTTTCTCTTCTTCAGCAACTTCCTTTTCTTCAGCAACAATTTCCTCTTCTGCAGTAGCAGCTTCC
*
65646219 TTGTCAACAATAGTGCCCTATTGATCAGCAAAAATATCATTTCGAACAAGCTATCAATCTTGTGT
131 TTGTCAACAATAGTGCCCTATTGATCAGCAAAAATATCATTTTGAACAAGCTATCAATCTTGTGT
65646284 AGACATTCCTCAAAGCCTATGGATTCTTCATCTTTGTCATTATCAGAGACTTGCACGATAGGAGG
196 AGACATTCCTCAAAGCCTATGGATTCTTCATCTTTGTCATTATCAGAGACTTGCACGATAGGAGG
65646349 AGATGCCACCAATCGGTCTCAATCTTTGAAGTCGTCATTTGTAAATGAATGCTTATAGTTTCAAA
261 AGATGCCACCAATCGGTCTCAATCTTTGAAGTCGTCATTTGTAAATGAATGCTTATAGTTTCAAA
65646414 TGATTGGTGGAAATACTGGGAAGTTCGGTATTATAGTTTC
326 TGATTGGTGGAAATACTGGGAAGTTCGGTATTATAGTTTC
*
65646454 AATATTTACACCCATAGATTCTAGTGTGGTGACAATATTCACATCAGAATCTTTCTCTTCTATTT
1 AATATTTACACCCACAGATTCTAGTGTGGTGACAATATTCACATCAGAATCTTTCTCTTCTATTT
* *
65646519 CTTTCTCTTCTTCAGCAACTTTCTTTTCTTCAGCAACAATTTCTTCTTCTGCAGTAGCAGCTTCC
66 CTTTCTCTTCTTCAGCAACTTCCTTTTCTTCAGCAACAATTTCCTCTTCTGCAGTAGCAGCTTCC
65646584 TTGTCAACAATAGTGCCCTATTGATCAGCAAAAATATCATTTTGAACAAGCTATCAATCTTGTGT
131 TTGTCAACAATAGTGCCCTATTGATCAGCAAAAATATCATTTTGAACAAGCTATCAATCTTGTGT
65646649 AGACATTCCTCAAAGCCTATGGATTCTTCATCTTTGTCATTATCAGAGACTTGCACGATAGGAGG
196 AGACATTCCTCAAAGCCTATGGATTCTTCATCTTTGTCATTATCAGAGACTTGCACGATAGGAGG
* *
65646714 AGATGCCACCCATCGGTCTCAATCTTTGAAGTCGTCATTTTTAAATGAATGCTTATAGTTTCAAA
261 AGATGCCACCAATCGGTCTCAATCTTTGAAGTCGTCATTTGTAAATGAATGCTTATAGTTTCAAA
65646779 TGATTGGTGGAAATACTGGGAAGTTCGGTATTATAGTTTC
326 TGATTGGTGGAAATACTGGGAAGTTCGGTATTATAGTTTC
65646819 AATATTTACACCCACAGATTCTAGTGTGGTGACAATATTCACATCAGAATCTTTCTCTTCTATTT
1 AATATTTACACCCACAGATTCTAGTGTGGTGACAATATTCACATCAGAATCTTTCTCTTCTATTT
65646884 CTTTCTCTTCTTCAGCAACTTCCTTTTCTTCAGCAACAATTTCCTCTTCTGCAGTAGCAGCTTCC
66 CTTTCTCTTCTTCAGCAACTTCCTTTTCTTCAGCAACAATTTCCTCTTCTGCAGTAGCAGCTTCC
65646949 TTGTCAACAATAGTGCCCTATTGATCAGCAAAAATATCATTTTGAACAAGCTATCAATCTTGTGT
131 TTGTCAACAATAGTGCCCTATTGATCAGCAAAAATATCATTTTGAACAAGCTATCAATCTTGTGT
* *
65647014 AGACATTCCTCAAAGCTTATGGATTCTTCATCTTTGTCATTATCAGAGACTTGCACGATAGGAGA
196 AGACATTCCTCAAAGCCTATGGATTCTTCATCTTTGTCATTATCAGAGACTTGCACGATAGGAGG
*
65647079 AGATGCCACCGATCGGTCTCAATCTTTGAAGTCGTCATTTGTAAATGAATGCTTATAGTTTCAAA
261 AGATGCCACCAATCGGTCTCAATCTTTGAAGTCGTCATTTGTAAATGAATGCTTATAGTTTCAAA
65647144 TGATTGGTGGAAATACTGGGAAGTTCGGTATTATAGTTTC
326 TGATTGGTGGAAATACTGGGAAGTTCGGTATTATAGTTTC
65647184 AATATTTACACCCACAGATTCTAGTGTGGTGACAATATTCACATCAGAATCTTTCTCTTCTATTT
1 AATATTTACACCCACAGATTCTAGTGTGGTGACAATATTCACATCAGAATCTTTCTCTTCTATTT
* *
65647249 CTTTCTCTTCTTCAGCAACTTCCTTTTCTTCAGCAACAATTTCCTCTTTTGCAATAGCAGCTTCC
66 CTTTCTCTTCTTCAGCAACTTCCTTTTCTTCAGCAACAATTTCCTCTTCTGCAGTAGCAGCTTCC
* *
65647314 TTGTCAACAATAGTGCCCTATTGATCAGCAAAAATACCATTTCGAACAAGCTATCAATCTTGTGT
131 TTGTCAACAATAGTGCCCTATTGATCAGCAAAAATATCATTTTGAACAAGCTATCAATCTTGTGT
*
65647379 AGACATTCCTCAAAGCCTATGGATTCTTCATTTTTGTCATTATCAGAGACTTGCACGAT-GAGAG
196 AGACATTCCTCAAAGCCTATGGATTCTTCATCTTTGTCATTATCAGAGACTTGCACGATAG-GAG
*
65647443 GAGATGCCACCGATCGGTCTCAATCTTTGAAGTCGTCATTTGTAAATGAATGCTTATAGTTTCAA
260 GAGATGCCACCAATCGGTCTCAATCTTTGAAGTCGTCATTTGTAAATGAATGCTTATAGTTTCAA
65647508 ATGATTGG
325 ATGATTGG
65647516 ACTGGGAAGT
Statistics
Matches: 1767, Mismatches: 24, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
364 1 0.00
365 1766 1.00
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (365 bp):
AATATTTACACCCACAGATTCTAGTGTGGTGACAATATTCACATCAGAATCTTTCTCTTCTATTT
CTTTCTCTTCTTCAGCAACTTCCTTTTCTTCAGCAACAATTTCCTCTTCTGCAGTAGCAGCTTCC
TTGTCAACAATAGTGCCCTATTGATCAGCAAAAATATCATTTTGAACAAGCTATCAATCTTGTGT
AGACATTCCTCAAAGCCTATGGATTCTTCATCTTTGTCATTATCAGAGACTTGCACGATAGGAGG
AGATGCCACCAATCGGTCTCAATCTTTGAAGTCGTCATTTGTAAATGAATGCTTATAGTTTCAAA
TGATTGGTGGAAATACTGGGAAGTTCGGTATTATAGTTTC
Found at i:65646568 original size:21 final size:19
Alignment explanation
Indices: 65646519--65646568 Score: 68
Period size: 18 Copynumber: 2.6 Consensus size: 19
65646509 TCTTCTATTT
65646519 CTTTC-TCTTCTTCAGCAA
1 CTTTCTTCTTCTTCAGCAA
65646537 CTTTCTT-TTCTTCAGCAA
1 CTTTCTTCTTCTTCAGCAA
65646555 CAATTTCTTCTTCT
1 C--TTTCTTCTTCT
65646569 GCAGTAGCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 17 0.61
19 1 0.04
20 6 0.21
21 4 0.14
ACGTcount: A:0.16, C:0.30, G:0.04, T:0.50
Consensus pattern (19 bp):
CTTTCTTCTTCTTCAGCAA
Found at i:65653943 original size:13 final size:13
Alignment explanation
Indices: 65653925--65653951 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
65653915 GTTCGGTAGA
65653925 GACACGCCCGTGT
1 GACACGCCCGTGT
65653938 GACACGCCCGTGT
1 GACACGCCCGTGT
65653951 G
1 G
65653952 CGATTACTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.37, G:0.33, T:0.15
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:65656055 original size:29 final size:28
Alignment explanation
Indices: 65656023--65656078 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
65656013 TACCCCATGG
65656023 TTTTACCTGTTTTCAAATAGGCCCCATAT
1 TTTTACCT-TTTTCAAATAGGCCCCATAT
** * *
65656052 TTTTGTCTTTTTTAAATTGGCCCCATA
1 TTTTACCTTTTTCAAATAGGCCCCATA
65656079 ACTTCGTTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 17 0.74
29 6 0.26
ACGTcount: A:0.21, C:0.21, G:0.11, T:0.46
Consensus pattern (28 bp):
TTTTACCTTTTTCAAATAGGCCCCATAT
Found at i:65656195 original size:3 final size:3
Alignment explanation
Indices: 65656155--65656179 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
65656145 TCACTTTTAC
65656155 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
65656180 GTGTTGTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:65656489 original size:33 final size:33
Alignment explanation
Indices: 65656433--65656512 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
65656423 TAGTTTCAAC
*
65656433 ATATATATATTATGTTTACTTTTAATACTACGTT
1 ATATATATA-TATTTTTACTTTTAATACTACGTT
*
65656467 ATGTATATATATTTTTACTTTTAATACTACGTT
1 ATATATATATATTTTTACTTTTAATACTACGTT
65656500 ATATATATATATT
1 ATATATATATATT
65656513 CATATATATT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
33 35 0.81
34 8 0.19
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.54
Consensus pattern (33 bp):
ATATATATATATTTTTACTTTTAATACTACGTT
Found at i:65656918 original size:35 final size:31
Alignment explanation
Indices: 65656853--65656944 Score: 94
Period size: 35 Copynumber: 2.8 Consensus size: 31
65656843 CTAGATTTTA
* *
65656853 TATTCTTATATGTATATTATTACATTTATTT
1 TATTCTTATATATATATTATTACATGTATTT
65656884 TATTCTTATCATATATATTATCAATACATGTATTT
1 TATTCTTAT-ATATATATTAT---TACATGTATTT
* *
65656919 TATTATATGTATATATATTATGTACA
1 TATTCT-TATATATATATTAT-TACA
65656945 CATATTAATA
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
31 9 0.18
32 10 0.20
33 4 0.08
35 26 0.51
36 2 0.04
ACGTcount: A:0.34, C:0.08, G:0.04, T:0.54
Consensus pattern (31 bp):
TATTCTTATATATATATTATTACATGTATTT
Found at i:65669215 original size:74 final size:71
Alignment explanation
Indices: 65669025--65669375 Score: 337
Period size: 74 Copynumber: 4.9 Consensus size: 71
65669015 TTTGGGTACT
* * * ** **
65669025 CTGAGGTATCTTTAATTCATGTTTTCAAAAATCAACTCATATTGCAAGAAATGAGTTGAGCCTCA
1 CTGAGGTATTTTTAATTTATG-TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTCAAGCCTCA
65669090 GGTCACA
65 GGTCACA
* ** *
65669097 CGCTGAGGTATTTTTAGTTTATGTTTCAAAAATTGACTCATATTGCGAGAGGTGAGTCAAGCCTT
1 --CTGAGGTATTTTTAATTTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTCAAGCCTC
65669162 AGGTCACA
64 AGGTCACA
* * **
65669170 CTGAGGTATTTTTAATTCCTGTTGTTTCAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCT
1 CTGAGGTATTTTTAATT--T-ATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTCAAGCCT
* * *
65669235 CAAGACACG
63 CAGGTCACA
* * * * * *
65669244 TTGAGGTAATTTCAATTTATG-TTCCAAAATCAACTCATATTGCGAAAGGTGAGTCAAGCCTCGG
1 CTGAGGTATTTTTAATTTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTCAAGCCTCAG
* *
65669308 GGCACG
66 GTCACA
* * * * * *
65669314 CTGAGGTATTTTTAGTTTATGTTT-AGAAAATTAACTAATCTTGCGAAAGGTGAGTTAAGCCT
1 CTGAGGTATTTTTAATTTATGTTTCA-AAAATCAACTCATATTGCGAGAGGTGAGTCAAGCCT
65669376 TTTAATTTCT
Statistics
Matches: 229, Mismatches: 43, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
70 58 0.25
71 52 0.23
72 1 0.00
73 43 0.19
74 75 0.33
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (71 bp):
CTGAGGTATTTTTAATTTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTCAAGCCTCAG
GTCACA
Found at i:65669322 original size:144 final size:144
Alignment explanation
Indices: 65669025--65669337 Score: 396
Period size: 144 Copynumber: 2.2 Consensus size: 144
65669015 TTTGGGTACT
*
65669025 CTGAGGTATCTTTAATTCATGTTTTCAAAAATCAACTCATATTGCAAGAAATGAGTTGAGCCTCA
1 CTGAGGTATTTTTAATTCATGTTTTCAAAAATCAACTCATATTGCAAGAAATGAGTTGAGCCTCA
* * * * ** *
65669090 GGTCACACGCTGAGGTATTTTTAGTTTATGTTTCAAAAATTGACTCATATTGCGAGAGGTGAGTC
66 AG-CACACGCTGAGGTAATTTCAATTTATGTTTCAAAAATCAACTCATATTGCGAAAGGTGAGTC
* *
65669155 AAGCCTTAGGTCACA
130 AAGCCTCAGGGCACA
* * * **
65669170 CTGAGGTATTTTTAATTCCTGTTGTTTCAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCT
1 CTGAGGTATTTTTAATTCATG-T-TTTCAAAAATCAACTCATATTGCAAGAAATGAGTTGAGCCT
* *
65669235 CAAG-ACACGTTGAGGTAATTTCAATTTATG-TTCCAAAATCAACTCATATTGCGAAAGGTGAGT
64 CAAGCACACGCTGAGGTAATTTCAATTTATGTTTCAAAAATCAACTCATATTGCGAAAGGTGAGT
* *
65669298 CAAGCCTCGGGGCACG
129 CAAGCCTCAGGGCACA
* *
65669314 CTGAGGTATTTTTAGTTTATGTTT
1 CTGAGGTATTTTTAATTCATGTTT
65669338 AGAAAATTAA
Statistics
Matches: 144, Mismatches: 22, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
142 2 0.01
143 1 0.01
144 59 0.41
145 41 0.28
146 1 0.01
147 40 0.28
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.34
Consensus pattern (144 bp):
CTGAGGTATTTTTAATTCATGTTTTCAAAAATCAACTCATATTGCAAGAAATGAGTTGAGCCTCA
AGCACACGCTGAGGTAATTTCAATTTATGTTTCAAAAATCAACTCATATTGCGAAAGGTGAGTCA
AGCCTCAGGGCACA
Found at i:65669543 original size:88 final size:88
Alignment explanation
Indices: 65669394--65669561 Score: 257
Period size: 88 Copynumber: 1.9 Consensus size: 88
65669384 CTGTTTTTCA
* * * *
65669394 AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAATTT
1 AAAATCAACTCATATTGCAAGAGATGAGTTGAGCCTCGGCTCACATGCTGAGCTATTTTCAAATT
*
65669459 CTGTTTTTCAAATTCCGTTCGTC
66 CTGTTATTCAAATTCCGTTCGTC
* *
65669482 AAAATCAACTCATATTGCAAGAGATGAGTTGAGCCTCGGGTCACATG-TCGAGGTATTTTCAAAT
1 AAAATCAACTCATATTGCAAGAGATGAGTTGAGCCTCGGCTCACATGCT-GAGCTATTTTCAAAT
65669546 TCTGTTATTCAAATTC
65 TCTGTTATTCAAATTC
65669562 TATTTTTAAT
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
87 1 0.01
88 71 0.99
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (88 bp):
AAAATCAACTCATATTGCAAGAGATGAGTTGAGCCTCGGCTCACATGCTGAGCTATTTTCAAATT
CTGTTATTCAAATTCCGTTCGTC
Found at i:65669995 original size:74 final size:72
Alignment explanation
Indices: 65669812--65669996 Score: 217
Period size: 72 Copynumber: 2.5 Consensus size: 72
65669802 CTACTTTTTC
* * * * *
65669812 AAAATCAGCTCATATTGCTAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
***
65669877 GTGTTTT
66 GTGTAAA
** * *
65669884 AATTTCAACTTATATGGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
65669949 GTTGTAAAA
66 G-TGT-AAA
* * *
65669958 AAAATCAACTCAGATTGCGAAAAGTGAGTTGAGCCTCAG
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
65669997 TTCACATGCT
Statistics
Matches: 92, Mismatches: 19, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
72 57 0.62
73 3 0.03
74 32 0.35
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (72 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
GTGTAAA
Found at i:65677513 original size:42 final size:42
Alignment explanation
Indices: 65677400--65677561 Score: 150
Period size: 43 Copynumber: 3.8 Consensus size: 42
65677390 CAAAAAGCTC
* * * *
65677400 GTACAATGCCAACTTCCCAGACGTGGTCTTATATGTAATCAA
1 GTACGATGCCAACGTCCCAGACGTGGTCTTACATGAAATCAA
*
65677442 ATATCGATGCC-ACTGTCCCAGACAG-GGTCTTACATGAAATCAA
1 GTA-CGATGCCAAC-GTCCCAGAC-GTGGTCTTACATGAAATCAA
* * *
65677485 GTAGGATGCCAACGTCCTAGACGTGGTCTTACACGTAAATCATAA
1 GTACGATGCCAACGTCCCAGACGTGGTCTTACATG-AAATC--AA
* * *
65677530 GT-CGATGCCAATGTCCTAGACGTGGCCTTACA
1 GTACGATGCCAACGTCCCAGACGTGGTCTTACA
65677562 CGATAACACA
Statistics
Matches: 100, Mismatches: 12, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
41 1 0.01
42 28 0.28
43 39 0.39
44 28 0.28
45 4 0.04
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (42 bp):
GTACGATGCCAACGTCCCAGACGTGGTCTTACATGAAATCAA
Found at i:65677560 original size:86 final size:85
Alignment explanation
Indices: 65677405--65677561 Score: 201
Period size: 86 Copynumber: 1.8 Consensus size: 85
65677395 AGCTCGTACA
* * * * *
65677405 ATGCCAACTTCCCAGACGTGGTCTTATATGTAATCAAATATCGATGCCACTGTCCCAGACAGGGT
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCAAATATCGATGCCAATGTCCCAGACAGGGC
65677470 CTTACATGAAATCAAGTAGG
66 CTTACATGAAATCAAGTAGG
* * *
65677490 ATGCCAACGTCCTAGACGTGGTCTTACACGTAAATCATAA-GTCGATGCCAATGTCCTAGAC-GT
1 ATGCCAACGTCCCAGACGTGGTCTTACACGT-AATCA-AATATCGATGCCAATGTCCCAGACAG-
65677553 GGCCTTACA
63 GGCCTTACA
65677562 CGATAACACA
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
85 28 0.46
86 31 0.51
87 2 0.03
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.25
Consensus pattern (85 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCAAATATCGATGCCAATGTCCCAGACAGGGC
CTTACATGAAATCAAGTAGG
Found at i:65688206 original size:42 final size:42
Alignment explanation
Indices: 65688093--65688252 Score: 125
Period size: 43 Copynumber: 3.8 Consensus size: 42
65688083 TCAAAAGCTC
* * *
65688093 GTACAATGCCAACGTCCCAGACGTGGTCTTA-TATGTAATTAA
1 GTACGATGCCAACGTCCCAGACGTGGTCTTACT-TGAAATCAA
* * *
65688135 ATATCGATGTC-ACTATCCCAAAGA-G-GGTCTTACTTGAAATCAA
1 GTA-CGATGCCAAC-GTCCC--AGACGTGGTCTTACTTGAAATCAA
*
65688178 GTACGATGCCAACGTCCCAGACGTGGTCTTACATGAAAATCATAA
1 GTACGATGCCAACGTCCCAGACGTGGTCTTACTTG-AAATC--AA
* *
65688223 GT-CGAT-CCAATGTACCAGACGTGGTCTTAC
1 GTACGATGCCAACGTCCCAGACGTGGTCTTAC
65688253 ATGATAACAC
Statistics
Matches: 95, Mismatches: 12, Indels: 21
0.74 0.09 0.16
Matches are distributed among these distances:
40 3 0.03
41 1 0.01
42 24 0.25
43 54 0.57
44 6 0.06
45 7 0.07
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.26
Consensus pattern (42 bp):
GTACGATGCCAACGTCCCAGACGTGGTCTTACTTGAAATCAA
Found at i:65688241 original size:43 final size:43
Alignment explanation
Indices: 65688160--65688256 Score: 128
Period size: 43 Copynumber: 2.3 Consensus size: 43
65688150 TCCCAAAGAG
* *
65688160 GGTCTTACTTG-AAATCAAGTACGATGCCAACGTCCCAGACGT
1 GGTCTTACATGAAAATCAAGTACGATGCCAACGTACCAGACGT
*
65688202 GGTCTTACATGAAAATCATAAGT-CGAT-CCAATGTACCAGACGT
1 GGTCTTACATGAAAATC--AAGTACGATGCCAACGTACCAGACGT
65688245 GGTCTTACATGA
1 GGTCTTACATGA
65688257 TAACACAATC
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
42 10 0.20
43 31 0.63
44 4 0.08
45 4 0.08
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.26
Consensus pattern (43 bp):
GGTCTTACATGAAAATCAAGTACGATGCCAACGTACCAGACGT
Found at i:65692403 original size:8 final size:8
Alignment explanation
Indices: 65692390--65692414 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
65692380 GACCTATACT
65692390 AATGTTAC
1 AATGTTAC
65692398 AATGTTAC
1 AATGTTAC
65692406 AATGTTAC
1 AATGTTAC
65692414 A
1 A
65692415 CCTATGAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (8 bp):
AATGTTAC
Found at i:65699336 original size:13 final size:13
Alignment explanation
Indices: 65699318--65699344 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
65699308 GCTCGATAGG
65699318 GACACGCCCGTGT
1 GACACGCCCGTGT
65699331 GACACGCCCGTGT
1 GACACGCCCGTGT
65699344 G
1 G
65699345 CAAGTGCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.37, G:0.33, T:0.15
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:65700546 original size:16 final size:16
Alignment explanation
Indices: 65700527--65700560 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
65700517 AATTTACCTA
65700527 ATATAAACATACCAAT
1 ATATAAACATACCAAT
65700543 ATATAAACATACCAAT
1 ATATAAACATACCAAT
65700559 AT
1 AT
65700561 TCAAATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.56, C:0.18, G:0.00, T:0.26
Consensus pattern (16 bp):
ATATAAACATACCAAT
Found at i:65700560 original size:14 final size:15
Alignment explanation
Indices: 65700521--65700557 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
65700511 ATTTAAAATT
*
65700521 TACCTAATATAAACA
1 TACCAAATATAAACA
65700536 TACCAATATATAAACA
1 TACCAA-ATATAAACA
65700552 TACCAA
1 TACCAA
65700558 TATTCAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.54, C:0.22, G:0.00, T:0.24
Consensus pattern (15 bp):
TACCAAATATAAACA
Found at i:65701747 original size:15 final size:16
Alignment explanation
Indices: 65701729--65701762 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
65701719 AGCGAGGCCT
*
65701729 TTAGGA-GCTGTACCC
1 TTAGGAGGCTGAACCC
65701744 TTAGGAGGCTGAACCC
1 TTAGGAGGCTGAACCC
65701760 TTA
1 TTA
65701763 TCTGAAGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (16 bp):
TTAGGAGGCTGAACCC
Found at i:65702353 original size:55 final size:54
Alignment explanation
Indices: 65702294--65702444 Score: 151
Period size: 55 Copynumber: 2.7 Consensus size: 54
65702284 TTTGTGGAGG
*
65702294 GTGCAACCATTGACCTTACGGTTAGGGTTTACGCAATATGAGATGC-TGACGGAAA
1 GTGCAACCATTGACCTTACGGTT-GGGTTTACGCAATATGAGATGCAT-ACAGAAA
* * * * * * * *
65702349 GTGCAACCATTGACCCTAAGGCCTGAGTTTACACAATATTATATGCATACAGAAG
1 GTGCAACCATTGACCTTACGG-TTGGGTTTACGCAATATGAGATGCATACAGAAA
* **
65702404 GTGCAACCGTTGACCTTACTACTTGGGTTTACGCAATATGA
1 GTGCAACCATTGACCTTAC-GGTTGGGTTTACGCAATATGA
65702445 AATACTAATG
Statistics
Matches: 75, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
55 73 0.97
56 2 0.03
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.27
Consensus pattern (54 bp):
GTGCAACCATTGACCTTACGGTTGGGTTTACGCAATATGAGATGCATACAGAAA
Found at i:65703321 original size:19 final size:19
Alignment explanation
Indices: 65703274--65703322 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 19
65703264 AGGTCCCAAA
65703274 TTTAT-TATTTTAGAAAATT
1 TTTATATATTTTA-AAAATT
*
65703293 TTTA-AAATTTT-AAAATT
1 TTTATATATTTTAAAAATT
65703310 CTTTATATATTTT
1 -TTTATATATTTT
65703323 TTAGTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 6 0.24
18 4 0.16
19 15 0.60
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (19 bp):
TTTATATATTTTAAAAATT
Found at i:65703385 original size:18 final size:19
Alignment explanation
Indices: 65703348--65703384 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
65703338 TTTTTTAAAA
*
65703348 TATAAA-ATTTGGAATTTT
1 TATAAATATTTAGAATTTT
65703366 TATAAATATTTAGAATTTT
1 TATAAATATTTAGAATTTT
65703385 AAAAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (19 bp):
TATAAATATTTAGAATTTT
Found at i:65706823 original size:27 final size:27
Alignment explanation
Indices: 65706775--65706933 Score: 157
Period size: 27 Copynumber: 5.9 Consensus size: 27
65706765 GCGAGGCTGC
* *
65706775 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTGTGGCAG-AGCCACCAGATA
65706802 CAGATATTGTGGCAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
* * *
65706828 CATATATATGTGGTAAAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
65706855 CAGATAATCGTGGCATAGCCACCAGA-A
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
*
65706882 CAGATATATGTGGTAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
*
65706909 CAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
65706934 GACGCTTCCT
Statistics
Matches: 110, Mismatches: 14, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
26 9 0.08
27 96 0.87
28 5 0.05
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.20
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:65706875 original size:54 final size:54
Alignment explanation
Indices: 65706793--65706933 Score: 230
Period size: 54 Copynumber: 2.6 Consensus size: 54
65706783 GTGACGAAGT
* *
65706793 CACCAGATACAGAT-ATTGTGGCAGAGCCACCAGAACATATATATGTGGTAAAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGTAAAGC
* *
65706847 CACCAGATCAGATAATCGTGGCATAGCCACCAGAACAGATATATGTGGTAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGTAAAGC
65706901 CACCAGATCAGATAATTGTGGCATAGCCACCAG
1 CACCAGATCAGATAATTGTGGCATAGCCACCAG
65706934 GACGCTTCCT
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
53 5 0.06
54 76 0.94
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.19
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGTAAAGC
Found at i:65707101 original size:28 final size:26
Alignment explanation
Indices: 65707039--65707112 Score: 85
Period size: 28 Copynumber: 2.8 Consensus size: 26
65707029 AAATTAACCC
** * *
65707039 TAGGGGTATAACGGTAATTTTGCACC
1 TAGGGGTATAATAGTAATTTTCCACA
65707065 TAGGGGTATAATAGTAATTTTCCATACA
1 TAGGGGTATAATAGTAATTTTCC--ACA
*
65707093 TAGGGGTATTATAGTAATTT
1 TAGGGGTATAATAGTAATTT
65707113 AACTGCTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
26 20 0.49
28 21 0.51
ACGTcount: A:0.31, C:0.09, G:0.23, T:0.36
Consensus pattern (26 bp):
TAGGGGTATAATAGTAATTTTCCACA
Found at i:65708591 original size:26 final size:26
Alignment explanation
Indices: 65708561--65708931 Score: 742
Period size: 26 Copynumber: 14.3 Consensus size: 26
65708551 TGAAATTCCC
65708561 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
65708587 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
65708613 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
65708639 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
65708665 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
65708691 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
65708717 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
65708743 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
65708769 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
65708795 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
65708821 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
65708847 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
65708873 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
65708899 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
65708925 ATCATGG
1 ATCATGG
65708932 TGTATCAATT
Statistics
Matches: 345, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 345 1.00
ACGTcount: A:0.35, C:0.27, G:0.08, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:65712873 original size:17 final size:17
Alignment explanation
Indices: 65712851--65712885 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
65712841 GCAATCTTTA
65712851 TAAAAAT-TTTTTGTTTT
1 TAAAAATCTTTTT-TTTT
65712868 TAAAAATCTTTTTTTTT
1 TAAAAATCTTTTTTTTT
65712885 T
1 T
65712886 GTAAACCCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (17 bp):
TAAAAATCTTTTTTTTT
Found at i:65713888 original size:27 final size:27
Alignment explanation
Indices: 65713840--65713998 Score: 175
Period size: 27 Copynumber: 5.9 Consensus size: 27
65713830 GCGAGGCTGC
* *
65713840 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTGTGGCAG-AGCCACCAGATA
65713867 CAGATATTGTGGCAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
65713893 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* * *
65713920 CAGATAATCGTGGCATAACCACCAGA-A
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
*
65713947 CAGATATATGTGGTAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
*
65713974 CAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
65713999 GAAGCTTCCT
Statistics
Matches: 113, Mismatches: 11, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
26 10 0.09
27 98 0.87
28 5 0.04
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:65713933 original size:54 final size:54
Alignment explanation
Indices: 65713858--65713998 Score: 230
Period size: 54 Copynumber: 2.6 Consensus size: 54
65713848 GTGACGAAGT
*
65713858 CACCAGATACAGAT-ATTGTGGCAGAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
* * *
65713912 CACCAGATCAGATAATCGTGGCATAACCACCAGAACAGATATATGTGGTAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
65713966 CACCAGATCAGATAATTGTGGCATAGCCACCAG
1 CACCAGATCAGATAATTGTGGCATAGCCACCAG
65713999 GAAGCTTCCT
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
53 5 0.06
54 75 0.94
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.18
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
Found at i:65715621 original size:26 final size:26
Alignment explanation
Indices: 65715591--65715958 Score: 727
Period size: 26 Copynumber: 14.2 Consensus size: 26
65715581 TGAAATTCCC
*
65715591 ATCATGGAACATTTACCTAACCCATT
1 ATCATGAAACATTTACCTAACCCATT
65715617 ATCATGAAACATTTACCTAACCCATT
1 ATCATGAAACATTTACCTAACCCATT
65715643 ATCATGAAACATTTACCTAACCCATT
1 ATCATGAAACATTTACCTAACCCATT
65715669 ATCATGAAACATTTACCTAACCCATT
1 ATCATGAAACATTTACCTAACCCATT
65715695 ATCATGAAACATTTACCTAACCCATT
1 ATCATGAAACATTTACCTAACCCATT
65715721 ATCATGAAACATTTACCTAACCCATT
1 ATCATGAAACATTTACCTAACCCATT
65715747 ATCATGAAACATTTACCTAACCCATT
1 ATCATGAAACATTTACCTAACCCATT
65715773 ATCATGAAACATTTACCTAACCCATT
1 ATCATGAAACATTTACCTAACCCATT
65715799 ATCATGAAACATTTACCTAACCCATT
1 ATCATGAAACATTTACCTAACCCATT
65715825 ATCATGAAACATTTACCTAACCCATT
1 ATCATGAAACATTTACCTAACCCATT
65715851 ATCATGAAACATTTACCTAACCCATT
1 ATCATGAAACATTTACCTAACCCATT
65715877 ATCATGAAACATTTACCTAACCCATT
1 ATCATGAAACATTTACCTAACCCATT
65715903 ATCATGAAACATTTACCTAACCCATT
1 ATCATGAAACATTTACCTAACCCATT
65715929 ATCATGAAACATTTACCTAACCCATT
1 ATCATGAAACATTTACCTAACCCATT
65715955 ATCA
1 ATCA
65715959 ATTTGTATCA
Statistics
Matches: 341, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 341 1.00
ACGTcount: A:0.38, C:0.27, G:0.04, T:0.31
Consensus pattern (26 bp):
ATCATGAAACATTTACCTAACCCATT
Found at i:65727766 original size:22 final size:23
Alignment explanation
Indices: 65727720--65727775 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
65727710 TATAAAACCT
65727720 AATAAAAA-TAAGCTTAAAGAAA
1 AATAAAAAGTAAGCTTAAAGAAA
*
65727742 AATAAAAAGT-AGACTTAAA-ACA
1 AATAAAAAGTAAG-CTTAAAGAAA
*
65727764 AATTAAAAGTAA
1 AATAAAAAGTAA
65727776 CAATATAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 21 0.72
23 8 0.28
ACGTcount: A:0.66, C:0.05, G:0.09, T:0.20
Consensus pattern (23 bp):
AATAAAAAGTAAGCTTAAAGAAA
Found at i:65733387 original size:26 final size:26
Alignment explanation
Indices: 65733357--65733724 Score: 682
Period size: 26 Copynumber: 14.2 Consensus size: 26
65733347 TGAAATGCCC
65733357 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
65733383 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
65733409 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
65733435 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
65733461 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
65733487 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
65733513 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
65733539 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
65733565 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
65733591 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
65733617 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
65733643 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
65733669 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
65733695 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
65733721 ATCA
1 ATCA
65733725 ATTTGTATCA
Statistics
Matches: 330, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 330 1.00
ACGTcount: A:0.36, C:0.27, G:0.06, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:65739137 original size:18 final size:19
Alignment explanation
Indices: 65739096--65739139 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
65739086 ATTTGAGTAC
65739096 TCCATTTCTCATTCCATTT
1 TCCATTTCTCATTCCATTT
* *
65739115 T-CATTTCTCGTT-TATTT
1 TCCATTTCTCATTCCATTT
65739132 TCCATTTC
1 TCCATTTC
65739140 AATATCAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 5 0.23
18 16 0.73
19 1 0.05
ACGTcount: A:0.14, C:0.27, G:0.02, T:0.57
Consensus pattern (19 bp):
TCCATTTCTCATTCCATTT
Found at i:65741631 original size:16 final size:16
Alignment explanation
Indices: 65741589--65741647 Score: 50
Period size: 16 Copynumber: 3.8 Consensus size: 16
65741579 ATATTCATGT
*
65741589 TATTTT-TAATTTA-A
1 TATTTTATATTTTATA
*
65741603 TATTTAATGATTTTATA
1 TATTTTAT-ATTTTATA
*
65741620 TATTTTATATTTTTTA
1 TATTTTATATTTTATA
* *
65741636 AAATTTATATTT
1 TATTTTATATTT
65741648 AGTTATCTTC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
14 5 0.14
15 1 0.03
16 22 0.61
17 8 0.22
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (16 bp):
TATTTTATATTTTATA
Found at i:65745176 original size:14 final size:14
Alignment explanation
Indices: 65745157--65745183 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
65745147 CAAGACAAAA
65745157 TAGTGGGGTCCTAG
1 TAGTGGGGTCCTAG
65745171 TAGTGGGGTCCTA
1 TAGTGGGGTCCTA
65745184 TCATGAGCTA
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:0.15, C:0.15, G:0.41, T:0.30
Consensus pattern (14 bp):
TAGTGGGGTCCTAG
Found at i:65745370 original size:216 final size:215
Alignment explanation
Indices: 65745021--65745432 Score: 621
Period size: 216 Copynumber: 1.9 Consensus size: 215
65745011 ACGGAGCCCG
*
65745021 CTCAAATCGTCAGCCCCAAGAACAAAAAGGACCGCGTGCTCCATAGACATCTGCCCAACAAGCCT
1 CTCAAATCGTCAGCCCCAAGAACAAAAAGGACCACGTGCTCCATAGACATCTGCCCAACAAGCCT
* * * *
65745086 GAAGTCTGCTGAGAATGTCAGTATTAGGTACAGAGAATGTCAGGGCTAGAGGTAATTGAGTCAAG
66 GAAGTCCGCTGAGAATGTCAGTATTAGGGACAGAGAATGTCAGGGCTAAAGGTAATGGAGTCAAG
* * *
65745151 ACAAAATAGTGGGGTCCTAGTAGTGGGGTCCTATCATGAGCTATAATAATATTTGTGACACACAT
131 ACAAAATAATGGGGTCCTACTAGTGGGGTCCTATCATGAGCTATAATAATATCTGTGACA-ACAT
65745216 GTCCAACAGGTATAGGTCCCA
195 GTCCAACAGGTATAGGTCCCA
** * * *
65745237 CTCAAATCG-CTAGCCCCAAGAACAAAAAGGACCACGTGCTCTGTAGACATGTGTCCAACAGGCC
1 CTCAAATCGTC-AGCCCCAAGAACAAAAAGGACCACGTGCTCCATAGACATCTGCCCAACAAGCC
* * *
65745301 T-AGAGTCCGCTGAGAATGTCAGTATTAGGGACAGAGAATGTTAGGGCTAAAGGTAGTGGAGTTA
65 TGA-AGTCCGCTGAGAATGTCAGTATTAGGGACAGAGAATGTCAGGGCTAAAGGTAATGGAGTCA
* *
65745365 AGACAAAATAATGGGGTCCTACTAGTGGGGTCCTATTATGAGCTGTAATAATATCTGTGACAACA
129 AGACAAAATAATGGGGTCCTACTAGTGGGGTCCTATCATGAGCTATAATAATATCTGTGACAACA
65745430 TGT
194 TGT
65745433 ATAAATACCT
Statistics
Matches: 176, Mismatches: 18, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
215 8 0.05
216 168 0.95
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (215 bp):
CTCAAATCGTCAGCCCCAAGAACAAAAAGGACCACGTGCTCCATAGACATCTGCCCAACAAGCCT
GAAGTCCGCTGAGAATGTCAGTATTAGGGACAGAGAATGTCAGGGCTAAAGGTAATGGAGTCAAG
ACAAAATAATGGGGTCCTACTAGTGGGGTCCTATCATGAGCTATAATAATATCTGTGACAACATG
TCCAACAGGTATAGGTCCCA
Found at i:65758351 original size:2 final size:2
Alignment explanation
Indices: 65758344--65758374 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
65758334 CTGTCTCACA
*
65758344 CT CT CT CT CT CT CG CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
65758375 CATGATATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.03, T:0.45
Consensus pattern (2 bp):
CT
Found at i:65760713 original size:14 final size:14
Alignment explanation
Indices: 65760694--65760725 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
65760684 TCCAATCACC
65760694 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
65760708 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
65760722 GGGC
1 GGGC
65760726 TAAATGACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.16, G:0.47, T:0.31
Consensus pattern (14 bp):
GGGCCAGTTTGGTT
Found at i:65765838 original size:14 final size:14
Alignment explanation
Indices: 65765819--65765850 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
65765809 TCCAATCACC
*
65765819 GGGCCAGTTTGGTT
1 GGGCCAGATTGGTT
65765833 GGGCCAGATTGGTT
1 GGGCCAGATTGGTT
65765847 GGGC
1 GGGC
65765851 TAAATGACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.16, G:0.47, T:0.28
Consensus pattern (14 bp):
GGGCCAGATTGGTT
Found at i:65770120 original size:22 final size:22
Alignment explanation
Indices: 65770095--65770138 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
65770085 AACCGACGAA
*
65770095 AAAACGTGTCAAAAGACAGACG
1 AAAACATGTCAAAAGACAGACG
65770117 AAAACATGTCAAAAGACAGACG
1 AAAACATGTCAAAAGACAGACG
65770139 GATCATAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.52, C:0.18, G:0.20, T:0.09
Consensus pattern (22 bp):
AAAACATGTCAAAAGACAGACG
Found at i:65773839 original size:19 final size:19
Alignment explanation
Indices: 65773815--65773853 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
65773805 CTTAGTAAGT
65773815 TCGTATACTTAACTTACCA
1 TCGTATACTTAACTTACCA
65773834 TCGTATACTTAACTTACCA
1 TCGTATACTTAACTTACCA
65773853 T
1 T
65773854 TCATACTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.26, G:0.05, T:0.38
Consensus pattern (19 bp):
TCGTATACTTAACTTACCA
Found at i:65776497 original size:42 final size:41
Alignment explanation
Indices: 65776450--65776549 Score: 114
Period size: 41 Copynumber: 2.4 Consensus size: 41
65776440 CGCTAGTAAG
*
65776450 AAAACGCCGCAAAAGATTAAAGC-TATAGCGGCGTTTATGACA
1 AAAACGCCGCAAAAGATTAAAGCAT-TAGAGGCGTTTATGA-A
* * *
65776492 AAAACGCTGCAAAAG-GTCAAGCATTAGAGGCGTTTATGAA
1 AAAACGCCGCAAAAGATTAAAGCATTAGAGGCGTTTATGAA
*
65776532 ACAAACGCCGCAATAGAT
1 A-AAACGCCGCAAAAGAT
65776550 CGAGAATTAG
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
40 2 0.04
41 31 0.65
42 15 0.31
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.18
Consensus pattern (41 bp):
AAAACGCCGCAAAAGATTAAAGCATTAGAGGCGTTTATGAA
Found at i:65776559 original size:41 final size:41
Alignment explanation
Indices: 65776450--65776564 Score: 108
Period size: 41 Copynumber: 2.8 Consensus size: 41
65776440 CGCTAGTAAG
* * *
65776450 AAAACGCCGCAAAAGATTAA-AGCTATAGCGGCGTTTATGACA
1 AAAACGCCGCAAAAGATCAAGA-AT-TAGAGGCGTTTATGACA
* * *
65776492 AAAACGCTGCAAAAGGTCAAGCATTAGAGGCGTTTATGA-A
1 AAAACGCCGCAAAAGATCAAGAATTAGAGGCGTTTATGACA
* * *
65776532 ACAAACGCCGCAATAGATCGAGAATTAGCGGCG
1 A-AAACGCCGCAAAAGATCAAGAATTAGAGGCG
65776565 CTTTTTAGAA
Statistics
Matches: 59, Mismatches: 12, Indels: 5
0.78 0.16 0.07
Matches are distributed among these distances:
40 2 0.03
41 39 0.66
42 18 0.31
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.17
Consensus pattern (41 bp):
AAAACGCCGCAAAAGATCAAGAATTAGAGGCGTTTATGACA
Found at i:65776901 original size:22 final size:22
Alignment explanation
Indices: 65776876--65776920 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
65776866 GTGATTAGAG
65776876 TTTAAAGTTTAGGGT-TTATTAT
1 TTTAAAG-TTAGGGTCTTATTAT
* *
65776898 TTTATAGTTATGGTCTTATTAT
1 TTTAAAGTTAGGGTCTTATTAT
65776920 T
1 T
65776921 GTTCATGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.24, C:0.02, G:0.16, T:0.58
Consensus pattern (22 bp):
TTTAAAGTTAGGGTCTTATTAT
Found at i:65777072 original size:7 final size:7
Alignment explanation
Indices: 65777060--65777130 Score: 56
Period size: 7 Copynumber: 10.4 Consensus size: 7
65777050 AATATATATA
65777060 TTTAGGG
1 TTTAGGG
65777067 TTTAGGG
1 TTTAGGG
*
65777074 TGTA-GG
1 TTTAGGG
*
65777080 TTTATGG
1 TTTAGGG
* * *
65777087 TCTAAGA
1 TTTAGGG
*
65777094 TTTAGTG
1 TTTAGGG
* *
65777101 TTTATGA
1 TTTAGGG
65777108 TTTAGGG
1 TTTAGGG
65777115 TTTAGGG
1 TTTAGGG
65777122 TTT-GGG
1 TTTAGGG
65777128 TTT
1 TTT
65777131 GATAGTTTAA
Statistics
Matches: 49, Mismatches: 14, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
6 11 0.22
7 38 0.78
ACGTcount: A:0.17, C:0.01, G:0.34, T:0.48
Consensus pattern (7 bp):
TTTAGGG
Found at i:65777415 original size:14 final size:15
Alignment explanation
Indices: 65777397--65777437 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
65777387 AGGGTTAAGG
65777397 GTTTAGTGTTTATAA
1 GTTTAGTGTTTATAA
*
65777412 -TTTAGGGTTTA-AA
1 GTTTAGTGTTTATAA
*
65777425 GTTTAGTATTTAT
1 GTTTAGTGTTTAT
65777438 GGGAAGGGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
13 2 0.10
14 19 0.90
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.54
Consensus pattern (15 bp):
GTTTAGTGTTTATAA
Found at i:65777417 original size:28 final size:27
Alignment explanation
Indices: 65777378--65777437 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
65777368 ATAACATCAT
* *
65777378 TTTATATTTAGGG-TTAAGGGTTTAGTG
1 TTTATATTTAGGGTTTAA-AGTTTAGTA
65777405 TTTATAATTTAGGGTTTAAAGTTTAGTA
1 TTTAT-ATTTAGGGTTTAAAGTTTAGTA
65777433 TTTAT
1 TTTAT
65777438 GGGAAGGGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 5 0.17
28 20 0.69
29 4 0.14
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.52
Consensus pattern (27 bp):
TTTATATTTAGGGTTTAAAGTTTAGTA
Found at i:65778194 original size:82 final size:82
Alignment explanation
Indices: 65777855--65778176 Score: 608
Period size: 82 Copynumber: 3.9 Consensus size: 82
65777845 ATTAGTAGCT
* * * *
65777855 TTTTTTAAAAAACACCGCTAATCCTCTAAATCTCCAATTAAAGCGACGCCATTTTCGTTAAACTA
1 TTTTTTAAAAAACGCCGCCAATCCACTAAATCTCCAATTAAAACGACGCCATTTTCGTTAAACTA
65777920 TTATGTTTTTTTCTGTG
66 TTATGTTTTTTTCTGTG
65777937 TTTTTTAAAAAACGCCGCCAATCCACTAAATCTCCAATTAAAACGACGCCATTTTCGTTAAACTA
1 TTTTTTAAAAAACGCCGCCAATCCACTAAATCTCCAATTAAAACGACGCCATTTTCGTTAAACTA
65778002 TTATGTTTTTTTCTGTG
66 TTATGTTTTTTTCTGTG
65778019 TTTTTTAAAAAACGCCGCCAATCCACTAAATCTCCAATTAAAACGACGCCATTTTCGTTAAACTA
1 TTTTTTAAAAAACGCCGCCAATCCACTAAATCTCCAATTAAAACGACGCCATTTTCGTTAAACTA
65778084 TTATGTTTTTTTCTGTG
66 TTATGTTTTTTTCTGTG
65778101 TTTTTTAAAAAACGCCGCCAATCCACTAAATCTCCAATTAAAACGACGCCATTTTCGTTAAACTA
1 TTTTTTAAAAAACGCCGCCAATCCACTAAATCTCCAATTAAAACGACGCCATTTTCGTTAAACTA
65778166 TTATGTTTTTT
66 TTATGTTTTTT
65778177 GTGGCGTTTC
Statistics
Matches: 236, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 236 1.00
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.38
Consensus pattern (82 bp):
TTTTTTAAAAAACGCCGCCAATCCACTAAATCTCCAATTAAAACGACGCCATTTTCGTTAAACTA
TTATGTTTTTTTCTGTG
Found at i:65778478 original size:30 final size:28
Alignment explanation
Indices: 65778417--65778478 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 28
65778407 TAAAATGTGT
* * *
65778417 ATTTAGTCCTTATATTTTAATTTGATTA
1 ATTTAGTCCTTATATTTTAAATCGATCA
*
65778445 ATTTAGTCCCTGTATTTTTTAAATCGATCA
1 ATTTAGT-CCT-TATATTTTAAATCGATCA
65778475 ATTT
1 ATTT
65778479 TATCTTTTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 7 0.25
29 3 0.11
30 18 0.64
ACGTcount: A:0.27, C:0.11, G:0.08, T:0.53
Consensus pattern (28 bp):
ATTTAGTCCTTATATTTTAAATCGATCA
Found at i:65779111 original size:23 final size:23
Alignment explanation
Indices: 65779078--65779121 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
65779068 ACGTTTTTTC
*
65779078 AAAAAACGCCGTAAAAAAACAAA
1 AAAAAAAGCCGTAAAAAAACAAA
65779101 AAAAAAAGCCGTAAAAAAACA
1 AAAAAAAGCCGTAAAAAAACA
65779122 TAATTGTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.70, C:0.16, G:0.09, T:0.05
Consensus pattern (23 bp):
AAAAAAAGCCGTAAAAAAACAAA
Done.