Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold1024
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1774716
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 201941 characters in sequence are not A, C, G, or T
File 4 of 5
Found at i:819793 original size:4 final size:4
Alignment explanation
Indices: 819786--819810 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
819776 CCGTCCGTTC
819786 GTCT GTCT GTCT GTCT GTCT GTCT G
1 GTCT GTCT GTCT GTCT GTCT GTCT G
819811 ACTTCAGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.28, T:0.48
Consensus pattern (4 bp):
GTCT
Found at i:820652 original size:25 final size:25
Alignment explanation
Indices: 820624--820704 Score: 99
Period size: 25 Copynumber: 3.2 Consensus size: 25
820614 AAGAAATAAG
*
820624 AATTACAAATTTTGAAAAATGTAAA
1 AATTGCAAATTTTGAAAAATGTAAA
* **
820649 AATTGCAAATTTTGAAAAAAGTATG
1 AATTGCAAATTTTGAAAAATGTAAA
* *
820674 AATTGCAAATTCTGAAAAATTGCAAA
1 AATTGCAAATTTTGAAAAA-TGTAAA
820700 AATTG
1 AATTG
820705 GAAGTGTTAA
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
25 39 0.85
26 7 0.15
ACGTcount: A:0.51, C:0.06, G:0.12, T:0.31
Consensus pattern (25 bp):
AATTGCAAATTTTGAAAAATGTAAA
Found at i:821137 original size:11 final size:11
Alignment explanation
Indices: 821121--821149 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
821111 CCTTCACTTG
821121 ACATGCAGCTT
1 ACATGCAGCTT
821132 ACATGCAGCTT
1 ACATGCAGCTT
821143 ACATGCA
1 ACATGCA
821150 ATTAAGAGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (11 bp):
ACATGCAGCTT
Found at i:828054 original size:22 final size:22
Alignment explanation
Indices: 828029--828077 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
828019 CTTACGCTCC
828029 TTCGCCATAGC-ACTCTCGCACT
1 TTCGCCATAGCAACT-TCGCACT
* *
828051 TTCGCCTTCGCAACTTCGCACT
1 TTCGCCATAGCAACTTCGCACT
828073 TTCGC
1 TTCGC
828078 ATCTTTGACG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.14, C:0.41, G:0.14, T:0.31
Consensus pattern (22 bp):
TTCGCCATAGCAACTTCGCACT
Found at i:830738 original size:2 final size:2
Alignment explanation
Indices: 830731--830757 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
830721 NNNNNNNNNN
830731 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
830758 TGTTTATGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:832494 original size:327 final size:330
Alignment explanation
Indices: 831869--832780 Score: 1183
Period size: 327 Copynumber: 2.8 Consensus size: 330
831859 GAAAGTTGGC
* *** * *
831869 ATTGGTACAAAAGTATACCCCACGGTATGGCATGCCTAAACAAATAGTGTGTTAAAATATCAAGG
1 ATTGGTACAAAAGTATATCCCAAAATATGGCATG-CTAAACAAATAGTGTGTTAAAATTTCAAGC
* *
831934 ATCTGCGATAAATAGTTGTTGAGAAATCTTTGGCGAAAATTCGTTTGG--ATTTAGGCTCAAAAT
65 ATCTGCGATAAATAGTTGTTGAGAAATCTTTGGCGAAAATTCGTTTGGAAATTTTGGCTTAAAAT
* * *
831997 AAACAAAGTCATC--TTAACAGTAAGTTGACGTCCGATTGGTACAAAAGTATATCTAATGACATG
130 AAAC-AAGTCATCATTTAACAGTAAGTTGACGTCCGATTGGTACAAAAGTATTTCGAATGAAATG
* *
832060 GCATGCCAAAGA-AAATAGTGTGTTAAAATTTCAAGCATCTACGATGAATAGTTGCTGAGAAATC
194 GCATTCCAAA-ACAAATAGTGTGTTAAAATTTCAAGCATCTACGATAAATAGTTGCTGAGAAATC
* * * *
832124 TTTGACGGATATTTGTTTGAAAATTTTGGCTAAAAAAAAACAAAGTCGTCATTTAACA-TGAAGT
258 TTTGACGGAAATTCGTTTGAAAATTTAGGCTAAAAAAAAACAAAGTCATCATTTAACAGT-AAGT
832188 TGACGTCCG
322 TGACGTCCG
832197 ATTGGTACAAAA-TATATCCCAAAATATGGCATGTCTAAACAAATAGTGTGTTAAAATTTCAAGC
1 ATTGGTACAAAAGTATATCCCAAAATATGGCATG-CTAAACAAATAGTGTGTTAAAATTTCAAGC
* *
832261 ATCTGCGATAAATAGATGTTGAGAAATCTTTGGCGAAAATTCGTTCGGAAATTTTGGCTTAAAAT
65 ATCTGCGATAAATAGTTGTTGAGAAATCTTTGGCGAAAATTCGTTTGGAAATTTTGGCTTAAAAT
832326 AAAC-AGTCATCATTTAACAGTAAGTTGACGTCCGATTGGTACAAAAGTATTTC-AATGAAATGG
130 AAACAAGTCATCATTTAACAGTAAGTTGACGTCCGATTGGTACAAAAGTATTTCGAATGAAATGG
* * *
832389 CATTCCAAAACAAATAGTGTGTTAAAATATCAAGCACCTACGATAAATAGTTGTTGAGAAATCTT
195 CATTCCAAAACAAATAGTGTGTTAAAATTTCAAGCATCTACGATAAATAGTTGCTGAGAAATCTT
* * * *
832454 TGGC-GAAATTCGTTTGGAAATTTAGGCTCAAAATAAACAAAGTCATCATTTAACAGTAAGTTGA
260 TGACGGAAATTCGTTTGAAAATTTAGGCTAAAAAAAAACAAAGTCATCATTTAACAGTAAGTTGA
832518 CGTCCG
325 CGTCCG
* * *
832524 ATTGGTGCAAAAGTATAT-CTAATGAA-ATGGCATGCCAAAGCAAATAGTGTGTTAAAATTTCAA
1 ATTGGTACAAAAGTATATCCCAA--AATATGGCATGCTAAA-CAAATAGTGTGTTAAAATTTCAA
* * * * * ** * * *
832587 GCATCTACAATAAATCGTTGCTGGGAAATCTTTGATGGAAATTTGTTTGAAAATTTTGG-TTAAA
63 GCATCTGCGATAAATAGTTGTTGAGAAATCTTTGGCGAAAATTCGTTTGGAAATTTTGGCTT-AA
* *
832651 AATAAACAAAGTCGTCATTTAACA-TGAAGTTGACGTCCCATTGGTACAAAAGTATATTCGAA--
127 AATAAAC-AAGTCATCATTTAACAGT-AAGTTGACGTCCGATTGGTACAAAAGTAT-TTCGAATG
* * *
832713 AATATGGCATGT-CTAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCTATAAATAGTTGCTGA
189 AA-ATGGCAT-TCCAAAACAAATAGTGTGTTAAAATTTCAAGCATCTACGATAAATAGTTGCTGA
832777 GAAA
252 GAAA
832781 AATGCGACAG
Statistics
Matches: 517, Mismatches: 49, Indels: 33
0.86 0.08 0.06
Matches are distributed among these distances:
327 176 0.34
328 175 0.34
329 59 0.11
330 44 0.09
331 60 0.12
332 3 0.01
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (330 bp):
ATTGGTACAAAAGTATATCCCAAAATATGGCATGCTAAACAAATAGTGTGTTAAAATTTCAAGCA
TCTGCGATAAATAGTTGTTGAGAAATCTTTGGCGAAAATTCGTTTGGAAATTTTGGCTTAAAATA
AACAAGTCATCATTTAACAGTAAGTTGACGTCCGATTGGTACAAAAGTATTTCGAATGAAATGGC
ATTCCAAAACAAATAGTGTGTTAAAATTTCAAGCATCTACGATAAATAGTTGCTGAGAAATCTTT
GACGGAAATTCGTTTGAAAATTTAGGCTAAAAAAAAACAAAGTCATCATTTAACAGTAAGTTGAC
GTCCG
Found at i:832707 original size:166 final size:165
Alignment explanation
Indices: 831895--832780 Score: 1127
Period size: 166 Copynumber: 5.4 Consensus size: 165
831885 ACCCCACGGT
* * * *
831895 ATGGCATGCCTAAACAAATAGTGTGTTAAAATATCAAGGATCTGCGATAAATAGTTGTTGAGAAA
1 ATGGCATGCC-AAACAAATAGTGTGTTAAAATTTCAAGCATCTACGATAAATAGTTGCTGAGAAA
* * * * *
831960 TCTTTGGCGAAAATTCGTTTG--GATTTAGGCTCAAAATAAACAAAGTCATC--TTAACAGTAAG
65 TCTTTGACGGAAATTCGTTTGAAAATTTTGGCTAAAAATAAACAAAGTCATCATTTAACAGTAAG
*
832021 TTGACGTCCGATTGGTACAAAAGTATATCTAATGAC
130 TTGACGTCCGATTGGTACAAAAGTATATCTAATGAA
* *
832057 ATGGCATGCCAAAGAAAATAGTGTGTTAAAATTTCAAGCATCTACGATGAATAGTTGCTGAGAAA
1 ATGGCATGCCAAA-CAAATAGTGTGTTAAAATTTCAAGCATCTACGATAAATAGTTGCTGAGAAA
* * * *
832122 TCTTTGACGGATATTTGTTTGAAAATTTTGGCTAAAAAAAAACAAAGTCGTCATTTAACA-TGAA
65 TCTTTGACGGAAATTCGTTTGAAAATTTTGGCTAAAAATAAACAAAGTCATCATTTAACAGT-AA
*
832186 GTTGACGTCCGATTGGTACAAAA-TATATCCCAA--AA
129 GTTGACGTCCGATTGGTACAAAAGTATAT-CTAATGAA
* * * *
832221 TATGGCATGTCTAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCGATAAATAGATGTTGAGAA
1 -ATGGCATG-CCAAACAAATAGTGTGTTAAAATTTCAAGCATCTACGATAAATAGTTGCTGAGAA
* * * * *
832286 ATCTTTGGCGAAAATTCGTTCGGAAATTTTGGCTTAAAATAAAC--AGTCATCATTTAACAGTAA
64 ATCTTTGACGGAAATTCGTTTGAAAATTTTGGCTAAAAATAAACAAAGTCATCATTTAACAGTAA
*
832349 GTTGACGTCCGATTGGTACAAAAGTATTTC-AATGAA
129 GTTGACGTCCGATTGGTACAAAAGTATATCTAATGAA
* * * *
832385 ATGGCATTCCAAAACAAATAGTGTGTTAAAATATCAAGCACCTACGATAAATAGTTGTTGAGAAA
1 ATGGCATGCC-AAACAAATAGTGTGTTAAAATTTCAAGCATCTACGATAAATAGTTGCTGAGAAA
* * * *
832450 TCTTTGGC-GAAATTCGTTTGGAAATTTAGGCTCAAAATAAACAAAGTCATCATTTAACAGTAAG
65 TCTTTGACGGAAATTCGTTTGAAAATTTTGGCTAAAAATAAACAAAGTCATCATTTAACAGTAAG
*
832514 TTGACGTCCGATTGGTGCAAAAGTATATCTAATGAA
130 TTGACGTCCGATTGGTACAAAAGTATATCTAATGAA
* * *
832550 ATGGCATGCCAAAGCAAATAGTGTGTTAAAATTTCAAGCATCTACAATAAATCGTTGCTGGGAAA
1 ATGGCATGCCAAA-CAAATAGTGTGTTAAAATTTCAAGCATCTACGATAAATAGTTGCTGAGAAA
* * * *
832615 TCTTTGATGGAAATTTGTTTGAAAATTTTGGTTAAAAATAAACAAAGTCGTCATTTAACA-TGAA
65 TCTTTGACGGAAATTCGTTTGAAAATTTTGGCTAAAAATAAACAAAGTCATCATTTAACAGT-AA
* *
832679 GTTGACGTCCCATTGGTACAAAAGTATATTCGAA--AA
129 GTTGACGTCCGATTGGTACAAAAGTATA-TCTAATGAA
* * *
832715 TATGGCATGTCTAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCTATAAATAGTTGCTGAGAA
1 -ATGGCATG-CCAAACAAATAGTGTGTTAAAATTTCAAGCATCTACGATAAATAGTTGCTGAGAA
832780 A
64 A
832781 AATGCGACAG
Statistics
Matches: 633, Mismatches: 68, Indels: 42
0.85 0.09 0.06
Matches are distributed among these distances:
161 3 0.00
162 105 0.17
163 105 0.17
164 82 0.13
165 164 0.26
166 166 0.26
167 8 0.01
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (165 bp):
ATGGCATGCCAAACAAATAGTGTGTTAAAATTTCAAGCATCTACGATAAATAGTTGCTGAGAAAT
CTTTGACGGAAATTCGTTTGAAAATTTTGGCTAAAAATAAACAAAGTCATCATTTAACAGTAAGT
TGACGTCCGATTGGTACAAAAGTATATCTAATGAA
Found at i:839512 original size:2 final size:2
Alignment explanation
Indices: 839505--839559 Score: 83
Period size: 2 Copynumber: 27.5 Consensus size: 2
839495 AAACACCATT
* **
839505 TA TA TA TA TA TA TA TA TA TN NN TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
839547 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
839560 GATGCTGTGT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:841352 original size:2 final size:2
Alignment explanation
Indices: 841345--841398 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
841335 AATATGTCAC
841345 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
841387 AG AG AG AG AG AG
1 AG AG AG AG AG AG
841399 NNNNNNNNNN
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:844860 original size:16 final size:16
Alignment explanation
Indices: 844841--844875 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
844831 TCACCAAGAC
844841 GAGGCATCACCTTTAT
1 GAGGCATCACCTTTAT
844857 GAGGCATCACCTTTAT
1 GAGGCATCACCTTTAT
844873 GAG
1 GAG
844876 ACCACATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.29
Consensus pattern (16 bp):
GAGGCATCACCTTTAT
Found at i:847360 original size:194 final size:194
Alignment explanation
Indices: 847031--847414 Score: 732
Period size: 194 Copynumber: 2.0 Consensus size: 194
847021 GTTCAAAACC
847031 ATGTAATGTCAGATCTACAAAGATCGACAAATATGATAAAATTATCTTCAAATTGCTGTCTGAGC
1 ATGTAATGTCAGATCTACAAAGATCGACAAATATGATAAAATTATCTTCAAATTGCTGTCTGAGC
* *
847096 GCCTTAAAGGCACCAATTTAATTTGATTTACTACTTTACATTTCAAAACGTCACAAAAATGCGTG
66 GCCTTAAAGGCACCAATTTAATTTGATTTACTACTTCACATTTCAAAACGTCACAAAAATACGTG
847161 CATTTGTTTACACGAAAAATTAAAGAATTGTTGGGTTTAAAGGGAAAAGTGAACAAAAATCATT
131 CATTTGTTTACACGAAAAATTAAAGAATTGTTGGGTTTAAAGGGAAAAGTGAACAAAAATCATT
847225 ATGTAATGTCAGATCTACAAAGATCGACAAATATGATAAAATTATCTTCAAATTGCTGTCTGAGC
1 ATGTAATGTCAGATCTACAAAGATCGACAAATATGATAAAATTATCTTCAAATTGCTGTCTGAGC
*
847290 GCCTTAAAGGCACCAATTTAATTTGATTTACTGCTTCACATTTCAAAACGTCACAAAAATACGTG
66 GCCTTAAAGGCACCAATTTAATTTGATTTACTACTTCACATTTCAAAACGTCACAAAAATACGTG
*
847355 CATTTGTTTACACGAAAAATTAAAGAATTGTTTGGTTTAAAGGGAAAAGTGAACAAAAAT
131 CATTTGTTTACACGAAAAATTAAAGAATTGTTGGGTTTAAAGGGAAAAGTGAACAAAAAT
847415 TATGACATTC
Statistics
Matches: 186, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
194 186 1.00
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (194 bp):
ATGTAATGTCAGATCTACAAAGATCGACAAATATGATAAAATTATCTTCAAATTGCTGTCTGAGC
GCCTTAAAGGCACCAATTTAATTTGATTTACTACTTCACATTTCAAAACGTCACAAAAATACGTG
CATTTGTTTACACGAAAAATTAAAGAATTGTTGGGTTTAAAGGGAAAAGTGAACAAAAATCATT
Found at i:848912 original size:16 final size:15
Alignment explanation
Indices: 848887--848916 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
848877 AATACATATT
848887 ACAAAACAAAAAAAA
1 ACAAAACAAAAAAAA
848902 ACAACAACAAAAAAA
1 ACAA-AACAAAAAAA
848917 CCCCAACAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (15 bp):
ACAAAACAAAAAAAA
Found at i:849273 original size:2 final size:2
Alignment explanation
Indices: 849266--849297 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
849256 ATTAAGGTAA
849266 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
849298 GGCGATGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:851350 original size:30 final size:30
Alignment explanation
Indices: 851311--851780 Score: 127
Period size: 30 Copynumber: 14.6 Consensus size: 30
851301 AACTATCTAC
* *
851311 TACATGTACTCAACAACTCTATTCTATTGT
1 TACAAGTACTCAACAACTATATTCTATTGT
* * **
851341 TACAAGTACTCATCAACTGTACACAACTATT-T
1 TACAAGTACTCAACAAC--TATA-TTCTATTGT
*
851373 AATACATGTACTCAACAACTATATTCTATTGT
1 --TACAAGTACTCAACAACTATATTCTATTGT
* * *
851405 TACAAGTACTCATCAACTGTACACAACTATCTACATGT
1 TACAAGTACTCAACAAC--T--A-TA-T-TCTA-TTGT
* * * *
851443 ACTACATGTACTCAACAATTATATTATATTTT
1 --TACAAGTACTCAACAACTATATTCTATTGT
* * * * ** *
851475 TACAAATACTCAGCATCTGTAGACAACTATCTAT
1 TACAAGTACTCAACAAC--TATA-TTCTAT-TGT
** * *
851509 TACATTTACTTAACAACTATATTCTATTAT
1 TACAAGTACTCAACAACTATATTCTATTGT
* * ** *
851539 TACAAGTACTCATCAACTGTACACAATTATCTAT
1 TACAAGTACTCAACAACTATATTC---TAT-TGT
*
851573 TACATGTACTCAACAACTATATTCTATTGTT
1 TACAAGTACTCAACAACTATATTCTATTG-T
* * ** *
851604 ATACAAGTACTCATCAACTGTACACAACTATTAAT
1 -TACAAGTACTCAACAAC--TATA-TTCTATT-GT
* * * *
851639 TACATGTACTCAACCATTATATTCTGA-TAT
1 TACAAGTACTCAACAACTATATTCT-ATTGT
* * * *
851669 TACAAATACTCAACAACTGTAGACATCTATGTAT
1 TACAAGTACTCAACAAC--TATA-TTCTAT-TGT
* * *
851703 TACATGTACTCAATAACTATATTCTACTGT
1 TACAAGTACTCAACAACTATATTCTATTGT
* ** * *
851733 T-CAAAGTACTCAACAACTGTACACAACTGT
1 TAC-AAGTACTCAACAACTATATTCTATTGT
*
851763 TACAAGTTCTCAACAACT
1 TACAAGTACTCAACAACT
851781 GTACATATTA
Statistics
Matches: 316, Mismatches: 86, Indels: 76
0.66 0.18 0.16
Matches are distributed among these distances:
29 1 0.00
30 117 0.37
31 21 0.07
32 42 0.13
33 17 0.05
34 86 0.27
35 8 0.03
36 2 0.01
37 4 0.01
38 4 0.01
40 14 0.04
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.35
Consensus pattern (30 bp):
TACAAGTACTCAACAACTATATTCTATTGT
Found at i:851351 original size:64 final size:64
Alignment explanation
Indices: 851249--851760 Score: 618
Period size: 64 Copynumber: 7.9 Consensus size: 64
851239 AAGAGGTAAG
** * * *
851249 CATGTACTTTACAACTATATTCT-TCTGTAACAATTACTCATCAACTGTACACAACTATCTACTA
1 CATGTACTCAACAACTATATTCTAT-TGTTACAAGTACTCATCAACTGTACACAACTATCTATTA
* * *
851313 CATGTACTCAACAACTCTATTCTATTGTTACAAGTACTCATCAACTGTACACAACTATTTAATA
1 CATGTACTCAACAACTATATTCTATTGTTACAAGTACTCATCAACTGTACACAACTATCTATTA
851377 CATGTACTCAACAACTATATTCTATTGTTACAAGTACTCATCAACTGTACACAACTATCTACATG
1 CATGTACTCAACAACTATATTCTATTGTTACAAGTACTCATCAACTGTACACAACTATCT--A--
851442 TACTA
62 T--TA
* * * * * * *
851447 CATGTACTCAACAATTATATTATATTTTTACAAATACTCAGCATCTGTAGACAACTATCTATTA
1 CATGTACTCAACAACTATATTCTATTGTTACAAGTACTCATCAACTGTACACAACTATCTATTA
* * * *
851511 CATTTACTTAACAACTATATTCTATTATTACAAGTACTCATCAACTGTACACAATTATCTATTA
1 CATGTACTCAACAACTATATTCTATTGTTACAAGTACTCATCAACTGTACACAACTATCTATTA
851575 CATGTACTCAACAACTATATTCTATTGTTATACAAGTACTCATCAACTGTACACAACTAT-TAAT
1 CATGTACTCAACAACTATATTCTATTG-T-TACAAGTACTCATCAACTGTACACAACTATCT-AT
851639 TA
63 TA
* * * * * * * *
851641 CATGTACTCAACCATTATATTCTGA-TATTACAAATACTCAACAACTGTAGACATCTATGTATTA
1 CATGTACTCAACAACTATATTCT-ATTGTTACAAGTACTCATCAACTGTACACAACTATCTATTA
* * *
851705 CATGTACTCAATAACTATATTCTACTGTT-CAAAGTACTCAACAACTGTACACAACT
1 CATGTACTCAACAACTATATTCTATTGTTAC-AAGTACTCATCAACTGTACACAACT
851761 GTTACAAGTT
Statistics
Matches: 389, Mismatches: 45, Indels: 28
0.84 0.10 0.06
Matches are distributed among these distances:
63 2 0.01
64 268 0.69
65 5 0.01
66 57 0.15
67 1 0.00
68 1 0.00
70 55 0.14
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.35
Consensus pattern (64 bp):
CATGTACTCAACAACTATATTCTATTGTTACAAGTACTCATCAACTGTACACAACTATCTATTA
Found at i:851513 original size:134 final size:130
Alignment explanation
Indices: 851249--851760 Score: 580
Period size: 134 Copynumber: 3.9 Consensus size: 130
851239 AAGAGGTAAG
** * * *
851249 CATGTACTTTACAACTATATTCT-TCTGTAACAATTACTCATCAACTGTACACAACTA--TC-TA
1 CATGTACTCAACAACTATATTCTAT-TATTACAAGTACTCATCAACTGTACACAACTATCTCATA
* * *
851310 CTACATGTACTCAACAACTCTATTCTATTGTTACAAGTACTCATCAACTGTACACAACTATTTAA
65 CTACATGTACTCAACAACTATATTCTATTTTTACAAGTACTCATCAACTGTACACAACTA-TTAT
851375 TA
129 TA
*
851377 CATGTACTCAACAACTATATTCTATTGTTACAAGTACTCATCAACTGTACACAACTATCTACATG
1 CATGTACTCAACAACTATATTCTATTATTACAAGTACTCATCAACTGTACACAACTATCT-CA--
* * * * * *
851442 TACTACATGTACTCAACAATTATATTATATTTTTACAAATACTCAGCATCTGTAGACAACTATCT
63 TACTACATGTACTCAACAACTATATTCTATTTTTACAAGTACTCATCAACTGTACACAACTAT-T
851507 ATTA
127 ATTA
* * *
851511 CATTTACTTAACAACTATATTCTATTATTACAAGTACTCATCAACTGTACACAATTATCT-AT--
1 CATGTACTCAACAACTATATTCTATTATTACAAGTACTCATCAACTGTACACAACTATCTCATAC
851573 TACATGTACTCAACAACTATATTCTATTGTTATACAAGTACTCATCAACTGTACACAACTATTAA
66 TACATGTACTCAACAACTATATTCTATT-TT-TACAAGTACTCATCAACTGTACACAACTATT-A
851638 TTA
128 TTA
* * * * * * *
851641 CATGTACTCAACCATTATATTCTGA-TATTACAAATACTCAACAACTGTAGACATCTATGT-AT-
1 CATGTACTCAACAACTATATTCT-ATTATTACAAGTACTCATCAACTGTACACAACTATCTCATA
* * * *
851703 -TACATGTACTCAATAACTATATTCTACTGTT-CAAAGTACTCAACAACTGTACACAACT
65 CTACATGTACTCAACAACTATATTCTATTTTTAC-AAGTACTCATCAACTGTACACAACT
851761 GTTACAAGTT
Statistics
Matches: 334, Mismatches: 37, Indels: 26
0.84 0.09 0.07
Matches are distributed among these distances:
127 1 0.00
128 102 0.31
129 5 0.01
130 108 0.32
131 2 0.01
132 1 0.00
133 1 0.00
134 114 0.34
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.35
Consensus pattern (130 bp):
CATGTACTCAACAACTATATTCTATTATTACAAGTACTCATCAACTGTACACAACTATCTCATAC
TACATGTACTCAACAACTATATTCTATTTTTACAAGTACTCATCAACTGTACACAACTATTATTA
Found at i:851587 original size:198 final size:194
Alignment explanation
Indices: 851278--851760 Score: 677
Period size: 198 Copynumber: 2.5 Consensus size: 194
851268 TTCTTCTGTA
* * * * *
851278 ACAATTACTCATCAACTGTACACAACTATCTACTACATGTACTCAACAACTCTATTCTATTGTTA
1 ACAAATACTCAACAACTGTAGACAACTATCTATTACATGTACTCAACAACTATATTCTATTGTTA
*
851343 CAAGTACTCATCAACTGTACACAACTATTTAATACATGTACTCAACAACTATATTCTATTG-T-T
66 CAAGTACTCATCAACTGTACACAACTATCTAATACATGTACTCAACAACTATATTCTATTGTTAT
851406 ACAAGTACTCATCAACTGTACACAACTATCTACATGTACTACATGTACTCAACAATTATATTAT-
131 ACAAGTACTCATCAACTGTACACAACTAT-TA-A--T--TACATGTACTCAACAATTATATTATG
*
851470 ATTTTT
190 A-TATT
* * * * *
851476 ACAAATACTCAGCATCTGTAGACAACTATCTATTACATTTACTTAACAACTATATTCTATTATTA
1 ACAAATACTCAACAACTGTAGACAACTATCTATTACATGTACTCAACAACTATATTCTATTGTTA
* *
851541 CAAGTACTCATCAACTGTACACAATTATCTATTACATGTACTCAACAACTATATTCTATTGTTAT
66 CAAGTACTCATCAACTGTACACAACTATCTAATACATGTACTCAACAACTATATTCTATTGTTAT
* *
851606 ACAAGTACTCATCAACTGTACACAACTATTAATTACATGTACTCAACCATTATATTCTGATATT
131 ACAAGTACTCATCAACTGTACACAACTATTAATTACATGTACTCAACAATTATATTATGATATT
* * * *
851670 ACAAATACTCAACAACTGTAGACATCTATGTATTACATGTACTCAATAACTATATTCTACTGTT-
1 ACAAATACTCAACAACTGTAGACAACTATCTATTACATGTACTCAACAACTATATTCTATTGTTA
*
851734 CAAAGTACTCAACAACTGTACACAACT
66 C-AAGTACTCATCAACTGTACACAACT
851761 GTTACAAGTT
Statistics
Matches: 255, Mismatches: 26, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
193 1 0.00
194 104 0.41
195 1 0.00
196 1 0.00
198 115 0.45
199 3 0.01
200 30 0.12
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.34
Consensus pattern (194 bp):
ACAAATACTCAACAACTGTAGACAACTATCTATTACATGTACTCAACAACTATATTCTATTGTTA
CAAGTACTCATCAACTGTACACAACTATCTAATACATGTACTCAACAACTATATTCTATTGTTAT
ACAAGTACTCATCAACTGTACACAACTATTAATTACATGTACTCAACAATTATATTATGATATT
Found at i:851781 original size:30 final size:30
Alignment explanation
Indices: 851668--852007 Score: 202
Period size: 30 Copynumber: 11.4 Consensus size: 30
851658 TATTCTGATA
* * *
851668 TTACAAATACTCAACAACTGTAGACATCTATG
1 TTACAAGTACTCAACAACTGTACACAAC--TG
* * * ** *
851700 TATTACATGTACTCAATAACTATATTCTACTG
1 --TTACAAGTACTCAACAACTGTACACAACTG
851732 TT-CAAAGTACTCAACAACTGTACACAACTG
1 TTAC-AAGTACTCAACAACTGTACACAACTG
* *
851762 TTACAAGTTCTCAACAACTGT--AC-A-TA
1 TTACAAGTACTCAACAACTGTACACAACTG
* *
851788 TTACAAGAACTC-A-AA-TGTACATAACTG
1 TTACAAGTACTCAACAACTGTACACAACTG
*
851815 TTACAA--ACTCAACAACTGTGCA-AAGCTG
1 TTACAAGTACTCAACAACTGTACACAA-CTG
* * * * *
851843 TAACAAGAACTAAACATCTCTACACAACTG
1 TTACAAGTACTCAACAACTGTACACAACTG
** * *
851873 CCACATGTACTCAA-ATACTGTACACAACAG
1 TTACAAGTACTCAACA-ACTGTACACAACTG
* *
851903 TTACAAGTACTCAAAAACAGTACAATCATAACTG
1 TTACAAGTACTCAACAACTGTAC-A-C--AACTG
** * * *
851937 TTACATTTACTTAACAACTGTACACAATTC
1 TTACAAGTACTCAACAACTGTACACAACTG
*
851967 TTACAAGTACTAAACAA-TGATACACAACTG
1 TTACAAGTACTCAACAACTG-TACACAACTG
851997 TTACAAGTACT
1 TTACAAGTACT
852008 GTTGAGTTGT
Statistics
Matches: 235, Mismatches: 51, Indels: 44
0.71 0.15 0.13
Matches are distributed among these distances:
23 3 0.01
24 2 0.01
25 6 0.03
26 13 0.06
27 12 0.05
28 15 0.06
29 4 0.02
30 128 0.54
31 5 0.02
32 4 0.02
33 1 0.00
34 42 0.18
ACGTcount: A:0.41, C:0.23, G:0.09, T:0.27
Consensus pattern (30 bp):
TTACAAGTACTCAACAACTGTACACAACTG
Found at i:852068 original size:2 final size:2
Alignment explanation
Indices: 852061--852090 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
852051 NNNNNNNNNN
852061 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
852091 AATTTGCAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:862046 original size:34 final size:34
Alignment explanation
Indices: 861879--862072 Score: 146
Period size: 34 Copynumber: 5.7 Consensus size: 34
861869 GAAGTCTGGA
* * * *
861879 GGAGAAAAGTAACACTAAGAGAAAAGTTGCACTT
1 GGAGAAAGGTTACACTTAGAGAAAAGTTGCACTG
* * * * *
861913 GAAAAAAGGTTAGA-TTAAAAGAAAAGTTGCACTT
1 GGAGAAAGGTTACACTT-AGAGAAAAGTTGCACTG
* * *
861947 GGAGAAA-GTTACA-ATA-AGAAAAGTTGTAATG
1 GGAGAAAGGTTACACTTAGAGAAAAGTTGCACTG
* * * * *
861978 GGAGAAAAGTTAATATGCTAAGAAAAAAGATGCACTG
1 GGAGAAAGGTT-ACA--CTTAGAGAAAAGTTGCACTG
862015 GGAGAAAGGTTACACTTAGAGAAAAGTTGCACTG
1 GGAGAAAGGTTACACTTAGAGAAAAGTTGCACTG
*
862049 TGAGAAAGGTTACACTATA-AGAAA
1 GGAGAAAGGTTACACT-TAGAGAAA
862073 GTCACTGGGT
Statistics
Matches: 125, Mismatches: 27, Indels: 16
0.74 0.16 0.10
Matches are distributed among these distances:
31 19 0.15
32 4 0.03
33 9 0.07
34 67 0.54
35 2 0.02
36 3 0.02
37 21 0.17
ACGTcount: A:0.47, C:0.08, G:0.24, T:0.21
Consensus pattern (34 bp):
GGAGAAAGGTTACACTTAGAGAAAAGTTGCACTG
Found at i:862053 original size:17 final size:17
Alignment explanation
Indices: 862002--862055 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
861992 ATGCTAAGAA
* *
862002 AAAAGATGCACTGGGAG
1 AAAAGTTGCACTGTGAG
* *
862019 AAAGGTTACACT-TAGAG
1 AAAAGTTGCACTGT-GAG
862036 AAAAGTTGCACTGTGAG
1 AAAAGTTGCACTGTGAG
862053 AAA
1 AAA
862056 GGTTACACTA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
17 28 0.97
18 1 0.03
ACGTcount: A:0.43, C:0.11, G:0.28, T:0.19
Consensus pattern (17 bp):
AAAAGTTGCACTGTGAG
Found at i:862064 original size:17 final size:17
Alignment explanation
Indices: 862010--862064 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
862000 AAAAAAGATG
*
862010 CACTGGGAGAAAGGTTA
1 CACTGTGAGAAAGGTTA
* *
862027 CACT-TAGAGAAAAGTTG
1 CACTGT-GAGAAAGGTTA
862044 CACTGTGAGAAAGGTTA
1 CACTGTGAGAAAGGTTA
862061 CACT
1 CACT
862065 ATAAGAAAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
17 30 0.97
18 1 0.03
ACGTcount: A:0.36, C:0.15, G:0.27, T:0.22
Consensus pattern (17 bp):
CACTGTGAGAAAGGTTA
Found at i:862071 original size:17 final size:16
Alignment explanation
Indices: 862017--862073 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
862007 ATGCACTGGG
862017 AGAAAGGTTACACTTA
1 AGAAAGGTTACACTTA
* * *
862033 GAGAAAAGTTGCACTGTG
1 -AGAAAGGTTACACT-TA
862051 AGAAAGGTTACACTATA
1 AGAAAGGTTACACT-TA
862068 AGAAAG
1 AGAAAG
862074 TCACTGGGTG
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
17 31 0.97
18 1 0.03
ACGTcount: A:0.44, C:0.11, G:0.25, T:0.21
Consensus pattern (16 bp):
AGAAAGGTTACACTTA
Found at i:865072 original size:2 final size:2
Alignment explanation
Indices: 865065--865148 Score: 159
Period size: 2 Copynumber: 41.5 Consensus size: 2
865055 GATAATAACT
865065 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
865107 GA GA GA GA GA GA GA GA GA GNA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA G-A GA GA GA GA GA GA GA GA GA GA G
865149 CATGGATGAT
Statistics
Matches: 81, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 79 0.98
3 2 0.02
ACGTcount: A:0.49, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:869236 original size:2 final size:2
Alignment explanation
Indices: 869229--869285 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
869219 ATCATAGGTA
869229 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
869271 AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG A
869286 CTTTTACTAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:870562 original size:33 final size:33
Alignment explanation
Indices: 870525--870603 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
870515 TTTTTGACGT
870525 AGAAAAATGACCCCCCCGGTCATTATTCTACGC
1 AGAAAAATGACCCCCCCGGTCATTATTCTACGC
*
870558 AGAAAAATGA-CCCCCCGGTCATTATTCTACGT
1 AGAAAAATGACCCCCCCGGTCATTATTCTACGC
870590 AGAAAAATGACCCC
1 AGAAAAATGACCCC
870604 TTTGCCTGAA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
32 31 0.70
33 13 0.30
ACGTcount: A:0.34, C:0.30, G:0.15, T:0.20
Consensus pattern (33 bp):
AGAAAAATGACCCCCCCGGTCATTATTCTACGC
Found at i:882659 original size:17 final size:17
Alignment explanation
Indices: 882637--882669 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
882627 ATATCATTCT
*
882637 ACATATTAATACATATA
1 ACATATCAATACATATA
882654 ACATATCAATACATAT
1 ACATATCAATACATAT
882670 CAATAACACG
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:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (17 bp):
ACATATCAATACATATA
Found at i:912989 original size:12 final size:12
Alignment explanation
Indices: 912974--913024 Score: 66
Period size: 12 Copynumber: 4.2 Consensus size: 12
912964 CGTCCGTCGA
912974 TCCGTCTGTCCG
1 TCCGTCTGTCCG
*
912986 TCCGTCCGTCCG
1 TCCGTCTGTCCG
*
912998 TCTGTCTGTCCG
1 TCCGTCTGTCCG
* *
913010 TCCATCTGTCTG
1 TCCGTCTGTCCG
913022 TCC
1 TCC
913025 CACTTCAGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.02, C:0.41, G:0.22, T:0.35
Consensus pattern (12 bp):
TCCGTCTGTCCG
Found at i:912993 original size:16 final size:16
Alignment explanation
Indices: 912964--913024 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
912954 CTTTCCTCTG
912964 CGTCCGTC-GATCCGTC
1 CGTCCGTCTG-TCCGTC
* *
912980 TGTCCGTCCGTCCGTC
1 CGTCCGTCTGTCCGTC
*
912996 CGTCTGTCTGTCCGTC
1 CGTCCGTCTGTCCGTC
* *
913012 CATCTGTCTGTCC
1 CGTCCGTCTGTCC
913025 CACTTCAGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
16 38 0.97
17 1 0.03
ACGTcount: A:0.03, C:0.41, G:0.23, T:0.33
Consensus pattern (16 bp):
CGTCCGTCTGTCCGTC
Found at i:913023 original size:4 final size:4
Alignment explanation
Indices: 912964--913012 Score: 55
Period size: 4 Copynumber: 12.2 Consensus size: 4
912954 CTTTCCTCTG
* * *
912964 CGTC CGT- CGATC CGTC TGTC CGTC CGTC CGTC CGTC TGTC TGTC CGTC
1 CGTC CGTC CG-TC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC
913012 C
1 C
913013 ATCTGTCTGT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
3 2 0.05
4 35 0.90
5 2 0.05
ACGTcount: A:0.02, C:0.43, G:0.24, T:0.31
Consensus pattern (4 bp):
CGTC
Found at i:913667 original size:7 final size:7
Alignment explanation
Indices: 913651--913685 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
913641 AGGCTTATTT
913651 GAGATTC
1 GAGATTC
*
913658 GAGGTTC
1 GAGATTC
913665 GAGATTC
1 GAGATTC
*
913672 GAAATTC
1 GAGATTC
913679 GAGATTC
1 GAGATTC
913686 ATAATAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (7 bp):
GAGATTC
Found at i:918504 original size:20 final size:19
Alignment explanation
Indices: 918464--918503 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
918454 GAATCAATTA
918464 TCCTATGGGAATTATCATTT
1 TCCTATGGGAATTAT-ATTT
918484 TCCTATGGGATATT-TATTT
1 TCCTATGGGA-ATTATATTT
918503 T
1 T
918504 TAAAGGTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 11 0.58
21 3 0.16
ACGTcount: A:0.23, C:0.12, G:0.15, T:0.50
Consensus pattern (19 bp):
TCCTATGGGAATTATATTT
Found at i:919012 original size:17 final size:17
Alignment explanation
Indices: 918990--919022 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
918980 TTATCGTATA
918990 ATTACCTTTCTGACTCT
1 ATTACCTTTCTGACTCT
919007 ATTACCTTTCTGACTC
1 ATTACCTTTCTGACTC
919023 GGGGCCCCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.30, G:0.06, T:0.45
Consensus pattern (17 bp):
ATTACCTTTCTGACTCT
Found at i:919044 original size:2 final size:2
Alignment explanation
Indices: 919037--919088 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
919027 CCCCAAATTT
919037 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
919079 GA GA GA GA GA
1 GA GA GA GA GA
919089 TTTTAGTTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:930563 original size:13 final size:13
Alignment explanation
Indices: 930545--930571 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
930535 TTCCTAGGCA
930545 CCTGATCCTACCT
1 CCTGATCCTACCT
930558 CCTGATCCTACCT
1 CCTGATCCTACCT
930571 C
1 C
930572 TATCTATCTT
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:0.48, G:0.07, T:0.30
Consensus pattern (13 bp):
CCTGATCCTACCT
Found at i:948645 original size:7 final size:7
Alignment explanation
Indices: 948633--948699 Score: 89
Period size: 7 Copynumber: 9.6 Consensus size: 7
948623 GAGAAGGATC
948633 ATTCGAG
1 ATTCGAG
948640 ATTCGAG
1 ATTCGAG
*
948647 ATTCGAA
1 ATTCGAG
*
948654 ATACGAG
1 ATTCGAG
*
948661 ATTCGAA
1 ATTCGAG
*
948668 ATACGAG
1 ATTCGAG
948675 ATTCGAG
1 ATTCGAG
*
948682 ATTCGAA
1 ATTCGAG
948689 ATTCGAG
1 ATTCGAG
948696 ATTC
1 ATTC
948700 AATATCTAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 50 1.00
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (7 bp):
ATTCGAG
Found at i:949202 original size:2 final size:2
Alignment explanation
Indices: 949195--949242 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
949185 TTGTCGATAT
949195 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
949237 GA GA GA
1 GA GA GA
949243 CAGACAGACA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:949247 original size:4 final size:4
Alignment explanation
Indices: 949240--949270 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
949230 AGAGAGAGAG
949240 AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGA
1 AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGA
949271 GTTTTGAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.23, G:0.26, T:0.00
Consensus pattern (4 bp):
AGAC
Found at i:951692 original size:7 final size:7
Alignment explanation
Indices: 951677--951743 Score: 89
Period size: 7 Copynumber: 9.6 Consensus size: 7
951667 TTTAGATATT
951677 GAATCTC
1 GAATCTC
*
951684 GAATTTC
1 GAATCTC
951691 GAATCTC
1 GAATCTC
951698 GAATCTC
1 GAATCTC
* *
951705 GTATTTC
1 GAATCTC
951712 GAATCTC
1 GAATCTC
* *
951719 GTATTTC
1 GAATCTC
951726 GAATCTC
1 GAATCTC
951733 GAATCTC
1 GAATCTC
951740 GAAT
1 GAAT
951744 GATCCTTCTC
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 50 1.00
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (7 bp):
GAATCTC
Found at i:951702 original size:21 final size:21
Alignment explanation
Indices: 951677--951743 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
951667 TTTAGATATT
951677 GAATCTCGAATTTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
*
951698 GAATCTCGTATTTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
* * *
951719 GTATTTCGAATCTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
951740 GAAT
1 GAAT
951744 GATCCTTCTC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (21 bp):
GAATCTCGAATTTCGAATCTC
Found at i:957347 original size:15 final size:15
Alignment explanation
Indices: 957327--957358 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
957317 TCCACTGGTA
957327 CATGTAGTGTAAATT
1 CATGTAGTGTAAATT
957342 CATGTAGTGTAAATT
1 CATGTAGTGTAAATT
957357 CA
1 CA
957359 AGTTGGTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (15 bp):
CATGTAGTGTAAATT
Found at i:959699 original size:2 final size:2
Alignment explanation
Indices: 959694--959749 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
959684 CACTCATATA
959694 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
959736 AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG
959750 GTGACTAAAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:960352 original size:2 final size:2
Alignment explanation
Indices: 960345--960392 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
960335 TACAACTTTC
960345 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
960387 A- AG AG A
1 AG AG AG A
960393 AAGTTTTTGA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:960981 original size:11 final size:11
Alignment explanation
Indices: 960964--960997 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
960954 CTACTACACC
960964 ACACGCTCGCT
1 ACACGCTCGCT
*
960975 GCACGCTCGCT
1 ACACGCTCGCT
960986 ACACGCTCGCT
1 ACACGCTCGCT
960997 A
1 A
960998 AACGGTTCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.18, C:0.44, G:0.21, T:0.18
Consensus pattern (11 bp):
ACACGCTCGCT
Found at i:961022 original size:21 final size:21
Alignment explanation
Indices: 960993--961099 Score: 142
Period size: 21 Copynumber: 5.1 Consensus size: 21
960983 GCTACACGCT
* *
960993 CGCTAAACGGTTCACACGAAA
1 CGCTGAACGGTTTACACGAAA
961014 CGCTGAACGGTTTACACGAAA
1 CGCTGAACGGTTTACACGAAA
* * * *
961035 CGCTGCACGCTTTGCCCGAAA
1 CGCTGAACGGTTTACACGAAA
* *
961056 CGCTAAACGATTTACACGAAA
1 CGCTGAACGGTTTACACGAAA
961077 CGCTGAACGGTTTACACGAAA
1 CGCTGAACGGTTTACACGAAA
961098 CG
1 CG
961100 ATTCTCGCAC
Statistics
Matches: 73, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 73 1.00
ACGTcount: A:0.33, C:0.28, G:0.21, T:0.18
Consensus pattern (21 bp):
CGCTGAACGGTTTACACGAAA
Found at i:961673 original size:122 final size:122
Alignment explanation
Indices: 961488--961728 Score: 428
Period size: 122 Copynumber: 2.0 Consensus size: 122
961478 AACTGAAATC
* * *
961488 GGTTTTTCAGTATTCGGCAGGATTTGTTTTTTCTTCTCATATTAATATTTTTCTTGGTGTCAGAG
1 GGTTTTTCAGTATTCGGCAGGATTTGTTTTTTCTTCTCACATTAATATTCTTATTGGTGTCAGAG
961553 AATACGATGTAAAAATACTAACTGTAAATAAACCTGTAATTATTCACATTGATATTT
66 AATACGATGTAAAAATACTAACTGTAAATAAACCTGTAATTATTCACATTGATATTT
* *
961610 GGTTTTTCAGTATTCGGCGGGATTTGTTTTTTCTTCTCACATTAATATTCTTATTGGTTTCAGAG
1 GGTTTTTCAGTATTCGGCAGGATTTGTTTTTTCTTCTCACATTAATATTCTTATTGGTGTCAGAG
*
961675 AATACGATGTAAAAATACTAACTGTAAATAAACCTGTAATTATTTACATTGATA
66 AATACGATGTAAAAATACTAACTGTAAATAAACCTGTAATTATTCACATTGATA
961729 ATTTTGAAAG
Statistics
Matches: 113, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
122 113 1.00
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.43
Consensus pattern (122 bp):
GGTTTTTCAGTATTCGGCAGGATTTGTTTTTTCTTCTCACATTAATATTCTTATTGGTGTCAGAG
AATACGATGTAAAAATACTAACTGTAAATAAACCTGTAATTATTCACATTGATATTT
Found at i:962719 original size:23 final size:21
Alignment explanation
Indices: 962689--962834 Score: 94
Period size: 21 Copynumber: 6.9 Consensus size: 21
962679 ACGGTTCTCG
* *
962689 CACGCTTTGCTCGAAACGATTTA
1 CACGCTTTGCCCGAAACG--CTA
*
962712 CACGCTTTGCCCGAAACGCTG
1 CACGCTTTGCCCGAAACGCTA
962733 CACGCTTTGCCCGAAACGCTA
1 CACGCTTTGCCCGAAACGCTA
* * * * *
962754 AACGGTTTACACGAAACGCTT
1 CACGCTTTGCCCGAAACGCTA
* ** *
962775 CACGATTCACACGAAACGCTA
1 CACGCTTTGCCCGAAACGCTA
* * * *
962796 AACGGTTTACACGAAACGCTA
1 CACGCTTTGCCCGAAACGCTA
* * * *
962817 AACGGTTTACACGAAACG
1 CACGCTTTGCCCGAAACG
962835 TTTCTCGCAC
Statistics
Matches: 107, Mismatches: 16, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
21 90 0.84
23 17 0.16
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (21 bp):
CACGCTTTGCCCGAAACGCTA
Found at i:962768 original size:21 final size:21
Alignment explanation
Indices: 962744--962834 Score: 146
Period size: 21 Copynumber: 4.3 Consensus size: 21
962734 ACGCTTTGCC
962744 CGAAACGCTAAACGGTTTACA
1 CGAAACGCTAAACGGTTTACA
** * *
962765 CGAAACGCTTCACGATTCACA
1 CGAAACGCTAAACGGTTTACA
962786 CGAAACGCTAAACGGTTTACA
1 CGAAACGCTAAACGGTTTACA
962807 CGAAACGCTAAACGGTTTACA
1 CGAAACGCTAAACGGTTTACA
962828 CGAAACG
1 CGAAACG
962835 TTTCTCGCAC
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 62 1.00
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.18
Consensus pattern (21 bp):
CGAAACGCTAAACGGTTTACA
Found at i:987878 original size:8 final size:8
Alignment explanation
Indices: 987865--987916 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
987855 TTTCCTCTGC
*
987865 GTCCGTCA
1 GTCCGTCT
987873 GTCCGTCT
1 GTCCGTCT
987881 GTCCGTCT
1 GTCCGTCT
*
987889 GTCCGTCC
1 GTCCGTCT
* *
987897 GTCAGTCC
1 GTCCGTCT
*
987905 GTCTGTCT
1 GTCCGTCT
987913 GTCC
1 GTCC
987917 CACTTCAGTT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 38 1.00
ACGTcount: A:0.04, C:0.38, G:0.25, T:0.33
Consensus pattern (8 bp):
GTCCGTCT
Found at i:987896 original size:12 final size:12
Alignment explanation
Indices: 987865--987916 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 12
987855 TTTCCTCTGC
* *
987865 GTCCGTCAGTCC
1 GTCCGTCCGTCT
*
987877 GTCTGTCCGTCT
1 GTCCGTCCGTCT
*
987889 GTCCGTCCGTCA
1 GTCCGTCCGTCT
*
987901 GTCCGTCTGTCT
1 GTCCGTCCGTCT
987913 GTCC
1 GTCC
987917 CACTTCAGTT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.04, C:0.38, G:0.25, T:0.33
Consensus pattern (12 bp):
GTCCGTCCGTCT
Found at i:987915 original size:4 final size:4
Alignment explanation
Indices: 987864--987907 Score: 52
Period size: 4 Copynumber: 11.0 Consensus size: 4
987854 CTTTCCTCTG
* * * *
987864 CGTC CGTC AGTC CGTC TGTC CGTC TGTC CGTC CGTC AGTC CGTC
1 CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC
987908 TGTCTGTCCC
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.05, C:0.41, G:0.25, T:0.30
Consensus pattern (4 bp):
CGTC
Found at i:990175 original size:113 final size:113
Alignment explanation
Indices: 989970--990194 Score: 346
Period size: 113 Copynumber: 2.0 Consensus size: 113
989960 GATAAGAACG
* *
989970 ATTATCCTGAATTTTTCTCTTTGCTTAATAGATTCCAACACGTTTTTGCCAAAGATGACTTTGAT
1 ATTATCATGAAGTTTTCTCTTTGCTTAATAGATTCCAACACGTTTTTGCCAAAGATGACTTTGAT
*
990035 TTAGAGCTATTTAATGAGGGGGGACTCATAAGATACACACTGATGAAA
66 TTAGAGCTATTTAATGAGGGGGAACTCATAAGATACACACTGATGAAA
*
990083 ATTATCATGAAGTTTTCTCTTTGTTTAATAGATTCCAACACG-TTTTGCCAAAGATGACTTTGAT
1 ATTATCATGAAGTTTTCTCTTTGCTTAATAGATTCCAACACGTTTTTGCCAAAGATGACTTTGAT
* * * *
990147 TTAGGGCTATTTAATG-GGGAGATAACTCATAAGATAGACATTGATGAA
66 TTAGAGCTATTTAATGAGGG-G-GAACTCATAAGATACACACTGATGAA
990195 GAAAGACCTA
Statistics
Matches: 102, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
111 3 0.03
112 38 0.37
113 61 0.60
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (113 bp):
ATTATCATGAAGTTTTCTCTTTGCTTAATAGATTCCAACACGTTTTTGCCAAAGATGACTTTGAT
TTAGAGCTATTTAATGAGGGGGAACTCATAAGATACACACTGATGAAA
Found at i:991924 original size:2 final size:2
Alignment explanation
Indices: 991917--991957 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
991907 CCATCTATAG
991917 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
991958 TAGTACGGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:999140 original size:2 final size:2
Alignment explanation
Indices: 999133--999174 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
999123 CTTCATTCCG
999133 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
999175 TATATATATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:999371 original size:1 final size:1
Alignment explanation
Indices: 999365--999392 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
999355 GTATAGAGCA
999365 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
999393 TCCGCCCTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1000120 original size:2 final size:2
Alignment explanation
Indices: 1000113--1000169 Score: 96
Period size: 2 Copynumber: 28.5 Consensus size: 2
1000103 CAATACATCG
* *
1000113 GA GA GA GA GA GA CA CA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1000155 GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA G
1000170 GGGGGGGGAC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.04, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1004680 original size:4 final size:4
Alignment explanation
Indices: 1004656--1004695 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
1004646 CTTTCCTCTG
* * *
1004656 CGTC CGTC AGTC CGTC TGTC CGTC CGTC CGTC CGTT CGTC
1 CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC
1004696 TGTCTGTCCC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.03, C:0.42, G:0.25, T:0.30
Consensus pattern (4 bp):
CGTC
Found at i:1004680 original size:12 final size:12
Alignment explanation
Indices: 1004665--1004704 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
1004655 GCGTCCGTCA
1004665 GTCCGTCTGTCC
1 GTCCGTCTGTCC
*
1004677 GTCCGTCCGTCC
1 GTCCGTCTGTCC
* *
1004689 GTTCGTCTGTCT
1 GTCCGTCTGTCC
1004701 GTCC
1 GTCC
1004705 CACTTCAGTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.00, C:0.40, G:0.25, T:0.35
Consensus pattern (12 bp):
GTCCGTCTGTCC
Found at i:1006496 original size:34 final size:33
Alignment explanation
Indices: 1006425--1006525 Score: 193
Period size: 33 Copynumber: 3.1 Consensus size: 33
1006415 GCATCATTCT
1006425 TTTTTTGATGTTCAGTGTAACATGAGAATTTTC
1 TTTTTTGATGTTCAGTGTAACATGAGAATTTTC
*
1006458 TTTTTTGATGTTCAGTGGAACATGAGAATTTTC
1 TTTTTTGATGTTCAGTGTAACATGAGAATTTTC
1006491 TTTTTTGATGTTCAGTGTAACATGAGAATTTTC
1 TTTTTTGATGTTCAGTGTAACATGAGAATTTTC
1006524 TT
1 TT
1006526 GGTTTAAATT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 66 1.00
ACGTcount: A:0.24, C:0.09, G:0.19, T:0.49
Consensus pattern (33 bp):
TTTTTTGATGTTCAGTGTAACATGAGAATTTTC
Found at i:1012511 original size:10 final size:10
Alignment explanation
Indices: 1012498--1012523 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1012488 GGCCTTGGCC
1012498 TCATTCCATA
1 TCATTCCATA
1012508 TCATTCCATA
1 TCATTCCATA
1012518 TCATTC
1 TCATTC
1012524 TTGACCTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.27, C:0.31, G:0.00, T:0.42
Consensus pattern (10 bp):
TCATTCCATA
Found at i:1018973 original size:2 final size:2
Alignment explanation
Indices: 1018966--1018997 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1018956 NNNNNNNNNN
1018966 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1018998 CAAAAAATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1024475 original size:17 final size:16
Alignment explanation
Indices: 1024453--1024500 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
1024443 AATATTTAAG
1024453 AAATAAGCGATATCAAA
1 AAATAA-CGATATCAAA
*
1024470 AAATAACG-TGTCAAA
1 AAATAACGATATCAAA
*
1024485 AAGATAAAGATATCAA
1 AA-ATAACGATATCAA
1024501 CAACCTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 8 0.31
16 7 0.27
17 11 0.42
ACGTcount: A:0.58, C:0.10, G:0.12, T:0.19
Consensus pattern (16 bp):
AAATAACGATATCAAA
Found at i:1025591 original size:7 final size:7
Alignment explanation
Indices: 1025579--1025607 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
1025569 AAATCTCTTC
1025579 TTCTTTT
1 TTCTTTT
1025586 TTCTTTT
1 TTCTTTT
1025593 TT-TTTT
1 TTCTTTT
1025599 TTCTTTT
1 TTCTTTT
1025606 TT
1 TT
1025608 TAAATTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (7 bp):
TTCTTTT
Found at i:1025598 original size:13 final size:13
Alignment explanation
Indices: 1025582--1025608 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1025572 TCTCTTCTTC
1025582 TTTTTTCTTTTTT
1 TTTTTTCTTTTTT
1025595 TTTTTTCTTTTTT
1 TTTTTTCTTTTTT
1025608 T
1 T
1025609 AAATTTTATC
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:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (13 bp):
TTTTTTCTTTTTT
Found at i:1032582 original size:19 final size:19
Alignment explanation
Indices: 1032558--1032642 Score: 125
Period size: 19 Copynumber: 4.5 Consensus size: 19
1032548 GGTTCAATCA
*
1032558 CGTGAACACGGTGTCACCC
1 CGTGAACACGGTGTCACTC
*
1032577 CGTGAACATGGTGTCACTC
1 CGTGAACACGGTGTCACTC
*
1032596 CGTGAACATGGTGTCACTC
1 CGTGAACACGGTGTCACTC
*
1032615 CGTGAACACGGTATCACTC
1 CGTGAACACGGTGTCACTC
*
1032634 CGCGAACAC
1 CGTGAACAC
1032643 AGTGACTATG
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 61 1.00
ACGTcount: A:0.24, C:0.32, G:0.25, T:0.20
Consensus pattern (19 bp):
CGTGAACACGGTGTCACTC
Found at i:1032694 original size:2 final size:2
Alignment explanation
Indices: 1032687--1032720 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1032677 CAGCACTTAC
1032687 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1032721 NTGTCACCCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1032746 original size:19 final size:19
Alignment explanation
Indices: 1032722--1032794 Score: 110
Period size: 19 Copynumber: 3.8 Consensus size: 19
1032712 GAGAGAGAGN
*
1032722 TGTCACCCCGTGAACATGG
1 TGTCACTCCGTGAACATGG
1032741 TGTCACTCCGTGAACATGG
1 TGTCACTCCGTGAACATGG
*
1032760 TGTCACTCCGTGAACACGG
1 TGTCACTCCGTGAACATGG
* *
1032779 TATCACTCCGCGAACA
1 TGTCACTCCGTGAACA
1032795 CAGTGACTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 50 1.00
ACGTcount: A:0.23, C:0.32, G:0.23, T:0.22
Consensus pattern (19 bp):
TGTCACTCCGTGAACATGG
Found at i:1032847 original size:2 final size:2
Alignment explanation
Indices: 1032840--1032900 Score: 72
Period size: 2 Copynumber: 31.0 Consensus size: 2
1032830 CAGCACTTAC
* *
1032840 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG NAG GG TG -G
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -AG AG AG AG
*
1032882 AG -G AG AG AG AG AC AG AG AG
1 AG AG AG AG AG AG AG AG AG AG
1032901 GGAGGGTGGG
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
1 2 0.04
2 48 0.92
3 2 0.04
ACGTcount: A:0.44, C:0.02, G:0.51, T:0.02
Consensus pattern (2 bp):
AG
Found at i:1032847 original size:153 final size:152
Alignment explanation
Indices: 1032568--1032873 Score: 603
Period size: 153 Copynumber: 2.0 Consensus size: 152
1032558 CGTGAACACG
1032568 GTGTCACCCCGTGAACATGGTGTCACTCCGTGAACATGGTGTCACTCCGTGAACACGGTATCACT
1 GTGTCACCCCGTGAACATGGTGTCACTCCGTGAACATGGTGTCACTCCGTGAACACGGTATCACT
1032633 CCGCGAACACAGTGACTATGTCATTATTTGATCATGTGATACCTCAGCACTTACAGAGAGAGAGA
66 CCGCGAACACAGTGACTATGTCATTATTTGATCATGTGATACCTCAGCACTTACAGAGAGAGAGA
1032698 GAGAGAGAGAGAGAGAGAGAGA
131 GAGAGAGAGAGAGAGAGAGAGA
1032720 GNTGTCACCCCGTGAACATGGTGTCACTCCGTGAACATGGTGTCACTCCGTGAACACGGTATCAC
1 G-TGTCACCCCGTGAACATGGTGTCACTCCGTGAACATGGTGTCACTCCGTGAACACGGTATCAC
1032785 TCCGCGAACACAGTGACTATGTCATTATTTGATCATGTGATACCTCAGCACTTACAGAGAGAGAG
65 TCCGCGAACACAGTGACTATGTCATTATTTGATCATGTGATACCTCAGCACTTACAGAGAGAGAG
1032850 AGAGAGAGAGAGAGAGAGAGAGA
130 AGAGAGAGAGAGAGAGAGAGAGA
1032873 G
1 G
1032874 NAGGGTGGAG
Statistics
Matches: 153, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
152 1 0.01
153 152 0.99
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (152 bp):
GTGTCACCCCGTGAACATGGTGTCACTCCGTGAACATGGTGTCACTCCGTGAACACGGTATCACT
CCGCGAACACAGTGACTATGTCATTATTTGATCATGTGATACCTCAGCACTTACAGAGAGAGAGA
GAGAGAGAGAGAGAGAGAGAGA
Found at i:1032915 original size:29 final size:29
Alignment explanation
Indices: 1032855--1032909 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
1032845 GAGAGAGAGA
* *
1032855 GAGAGAGAGAGAGAGAGAGNAGGGTGGAG
1 GAGAGAGAGACAGAGAGAGGAGGGTGGAG
1032884 GAGAGAGAGACAGAGAG-GGAGGGTGG
1 GAGAGAGAGACAGAGAGAGGAGGGTGG
1032910 GTGGAGGAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.36, C:0.02, G:0.56, T:0.04
Consensus pattern (29 bp):
GAGAGAGAGACAGAGAGAGGAGGGTGGAG
Found at i:1035031 original size:14 final size:14
Alignment explanation
Indices: 1035014--1035046 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1035004 TAATGAACAA
1035014 CATTTATTTAAAAC
1 CATTTATTTAAAAC
*
1035028 CATTTATTTACAAC
1 CATTTATTTAAAAC
1035042 CATTT
1 CATTT
1035047 TGATATTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.36, C:0.18, G:0.00, T:0.45
Consensus pattern (14 bp):
CATTTATTTAAAAC
Found at i:1035597 original size:2 final size:2
Alignment explanation
Indices: 1035590--1035631 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1035580 TTAAAAGTAT
1035590 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1035632 TTTTCAGTCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1036887 original size:25 final size:25
Alignment explanation
Indices: 1036847--1036982 Score: 191
Period size: 25 Copynumber: 5.4 Consensus size: 25
1036837 TAAATATATA
1036847 TAGCCCCTACTATTTCACTTCGTTG
1 TAGCCCCTACTATTTCACTTCGTTG
* *
1036872 TAGCCCCAACTGTTTCACTTCGTTG
1 TAGCCCCTACTATTTCACTTCGTTG
* **
1036897 TAGCCCTTACTATTTCACTTTATTG
1 TAGCCCCTACTATTTCACTTCGTTG
*
1036922 TAGCCCCTACTTTTTCACTTCGTTG
1 TAGCCCCTACTATTTCACTTCGTTG
* **
1036947 TAGCTCCTACTATTTCACTTTATTG
1 TAGCCCCTACTATTTCACTTCGTTG
1036972 TAGCCCCTACT
1 TAGCCCCTACT
1036983 TAGCCCCTAC
Statistics
Matches: 95, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 95 1.00
ACGTcount: A:0.17, C:0.30, G:0.11, T:0.42
Consensus pattern (25 bp):
TAGCCCCTACTATTTCACTTCGTTG
Found at i:1036908 original size:50 final size:50
Alignment explanation
Indices: 1036847--1037198 Score: 398
Period size: 50 Copynumber: 6.8 Consensus size: 50
1036837 TAAATATATA
*
1036847 TAGCCCCTACTATTTCACTTCGTTGTAGCCCCAACTGTTTCACTTCGTTG
1 TAGCCCCTACTATTTCACTTCGTTGTAGCCCCTACTGTTTCACTTCGTTG
* ** *
1036897 TAGCCCTTACTATTTCACTTTATTGTAGCCCCTACTTTTTCACTTCGTTG
1 TAGCCCCTACTATTTCACTTCGTTGTAGCCCCTACTGTTTCACTTCGTTG
* * *
1036947 TAGCTCCTACTATTTCACTTTATTGTAGCCCCTACTTAGCCCCTACTGTTTCACTTCGTTG
1 TAGCCCCTACTATTTCAC--T-TCGT------T--GTAGCCCCTACTGTTTCACTTCGTTG
* *
1037008 TAGCCCCTACTATTTCACTTCGTTGTATCCCCTACTGTTTCACTTCATTG
1 TAGCCCCTACTATTTCACTTCGTTGTAGCCCCTACTGTTTCACTTCGTTG
* * *
1037058 TAGCCCCTACTTTTTCACCTCGTTGTAGCCCCTACTGTTTCACTTCGTTA
1 TAGCCCCTACTATTTCACTTCGTTGTAGCCCCTACTGTTTCACTTCGTTG
* * * * * *
1037108 TGGGCCCTACTGTTTCACTTCGTTATGGGCCCTACTGTTTCACTTCGTTG
1 TAGCCCCTACTATTTCACTTCGTTGTAGCCCCTACTGTTTCACTTCGTTG
* * * *
1037158 TAGCCCGTATTAGTTCACTTCGTTGTAGCCCCTACTATTTC
1 TAGCCCCTACTATTTCACTTCGTTGTAGCCCCTACTGTTTC
1037199 TTTTCATTGT
Statistics
Matches: 253, Mismatches: 38, Indels: 22
0.81 0.12 0.07
Matches are distributed among these distances:
50 202 0.80
52 2 0.01
53 3 0.01
58 3 0.01
59 2 0.01
61 41 0.16
ACGTcount: A:0.15, C:0.31, G:0.13, T:0.41
Consensus pattern (50 bp):
TAGCCCCTACTATTTCACTTCGTTGTAGCCCCTACTGTTTCACTTCGTTG
Found at i:1036938 original size:75 final size:75
Alignment explanation
Indices: 1036847--1037209 Score: 377
Period size: 75 Copynumber: 4.7 Consensus size: 75
1036837 TAAATATATA
* *
1036847 TAGCCCCTACTATTTCACTTCGTTGTAGCCCCAACTGTTTCACTTCGTTGTAGCCCTTACTATTT
1 TAGCCCCTACTATTTCACTTCGTTGTAGCCCCTACTGTTTCACTTCATTGTAGCCCTTACTATTT
**
1036912 CACTTTATTG
66 CACTTCGTTG
* * * *
1036922 TAGCCCCTACTTTTTCACTTCGTTGTAGCTCCTACTATTTCACTTTATTGTAGCCCCTACTTAGC
1 TAGCCCCTACTATTTCACTTCGTTGTAGCCCCTACTGTTTCACTTCATTGTAG--CC--CTTA--
1036987 CCCTACTGTTTCACTTCGTTG
60 --CTA---TTTCACTTCGTTG
* * *
1037008 TAGCCCCTACTATTTCACTTCGTTGTATCCCCTACTGTTTCACTTCATTGTAGCCCCTACTTTTT
1 TAGCCCCTACTATTTCACTTCGTTGTAGCCCCTACTGTTTCACTTCATTGTAGCCCTTACTATTT
*
1037073 CACCTCGTTG
66 CACTTCGTTG
* * * * * * * *
1037083 TAGCCCCTACTGTTTCACTTCGTTATGGGCCCTACTGTTTCACTTCGTTATGGGCCC-TACTGTT
1 TAGCCCCTACTATTTCACTTCGTTGTAGCCCCTACTGTTTCACTTCATTGT-AGCCCTTACTATT
1037147 TCACTTCGTTG
65 TCACTTCGTTG
* * * * **
1037158 TAGCCCGTATTAGTTCACTTCGTTGTAGCCCCTACTATTTCTTTTCATTGTA
1 TAGCCCCTACTATTTCACTTCGTTGTAGCCCCTACTGTTTCACTTCATTGTA
1037210 CATCGAAGTA
Statistics
Matches: 237, Mismatches: 39, Indels: 25
0.79 0.13 0.08
Matches are distributed among these distances:
75 158 0.67
76 4 0.02
77 2 0.01
78 2 0.01
79 4 0.02
82 3 0.01
83 3 0.01
84 2 0.01
86 59 0.25
ACGTcount: A:0.15, C:0.30, G:0.13, T:0.42
Consensus pattern (75 bp):
TAGCCCCTACTATTTCACTTCGTTGTAGCCCCTACTGTTTCACTTCATTGTAGCCCTTACTATTT
CACTTCGTTG
Found at i:1036992 original size:36 final size:36
Alignment explanation
Indices: 1036947--1037018 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
1036937 CACTTCGTTG
* *
1036947 TAGCTCCTACTATTTCACTTTATTGTAGCCCCTACT
1 TAGCCCCTACTATTTCACTTCATTGTAGCCCCTACT
* *
1036983 TAGCCCCTACTGTTTCACTTCGTTGTAGCCCCTACT
1 TAGCCCCTACTATTTCACTTCATTGTAGCCCCTACT
1037019 ATTTCACTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.17, C:0.33, G:0.11, T:0.39
Consensus pattern (36 bp):
TAGCCCCTACTATTTCACTTCATTGTAGCCCCTACT
Found at i:1037017 original size:61 final size:61
Alignment explanation
Indices: 1036922--1037043 Score: 199
Period size: 61 Copynumber: 2.0 Consensus size: 61
1036912 CACTTTATTG
* * *
1036922 TAGCCCCTACTTTTTCACTTCGTTGTAGCTCCTACTATTTCACTTTATTGTAGCCCCTACT
1 TAGCCCCTACTGTTTCACTTCGTTGTAGCCCCTACTATTTCACTTCATTGTAGCCCCTACT
* *
1036983 TAGCCCCTACTGTTTCACTTCGTTGTAGCCCCTACTATTTCACTTCGTTGTATCCCCTACT
1 TAGCCCCTACTGTTTCACTTCGTTGTAGCCCCTACTATTTCACTTCATTGTAGCCCCTACT
1037044 GTTTCACTTC
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 56 1.00
ACGTcount: A:0.16, C:0.33, G:0.11, T:0.41
Consensus pattern (61 bp):
TAGCCCCTACTGTTTCACTTCGTTGTAGCCCCTACTATTTCACTTCATTGTAGCCCCTACT
Found at i:1037042 original size:86 final size:86
Alignment explanation
Indices: 1036897--1037069 Score: 265
Period size: 86 Copynumber: 2.0 Consensus size: 86
1036887 CACTTCGTTG
* * * *
1036897 TAGCCCTTACTATTTCACTTTATTGTAGCCCCTACTTTTTCACTTCGTTGTAGCTCCTACTATTT
1 TAGCCCCTACTATTTCACTTCATTGTAGCCCCTACTATTTCACTTCGTTGTAGCCCCTACTATTT
*
1036962 CACTTTATTGTAGCCCCTACT
66 CACTTCATTGTAGCCCCTACT
* * * *
1036983 TAGCCCCTACTGTTTCACTTCGTTGTAGCCCCTACTATTTCACTTCGTTGTATCCCCTACTGTTT
1 TAGCCCCTACTATTTCACTTCATTGTAGCCCCTACTATTTCACTTCGTTGTAGCCCCTACTATTT
1037048 CACTTCATTGTAGCCCCTACT
66 CACTTCATTGTAGCCCCTACT
1037069 T
1 T
1037070 TTTCACCTCG
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
86 78 1.00
ACGTcount: A:0.16, C:0.31, G:0.10, T:0.42
Consensus pattern (86 bp):
TAGCCCCTACTATTTCACTTCATTGTAGCCCCTACTATTTCACTTCGTTGTAGCCCCTACTATTT
CACTTCATTGTAGCCCCTACT
Found at i:1037067 original size:111 final size:111
Alignment explanation
Indices: 1036872--1037093 Score: 336
Period size: 111 Copynumber: 2.0 Consensus size: 111
1036862 CACTTCGTTG
* * *
1036872 TAGCCCCAACTGTTTCACTTCGTTGTAGCCCTTACTATTTCACTTTATTGTAGCCCCTACTTTTT
1 TAGCCCCAACTGTTTCACTTCGTTGTAGCCCCTACTATTTCACTTCATTGTAGCCCCTACTGTTT
* * * *
1036937 CACTTCGTTGTAGCTCCTACTATTTCACTTTATTGTAGCCCCTACT
66 CACTTCATTGTAGCCCCTACTATTTCACCTCATTGTAGCCCCTACT
* * *
1036983 TAGCCCCTACTGTTTCACTTCGTTGTAGCCCCTACTATTTCACTTCGTTGTATCCCCTACTGTTT
1 TAGCCCCAACTGTTTCACTTCGTTGTAGCCCCTACTATTTCACTTCATTGTAGCCCCTACTGTTT
* *
1037048 CACTTCATTGTAGCCCCTACTTTTTCACCTCGTTGTAGCCCCTACT
66 CACTTCATTGTAGCCCCTACTATTTCACCTCATTGTAGCCCCTACT
1037094 GTTTCACTTC
Statistics
Matches: 99, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
111 99 1.00
ACGTcount: A:0.16, C:0.32, G:0.11, T:0.41
Consensus pattern (111 bp):
TAGCCCCAACTGTTTCACTTCGTTGTAGCCCCTACTATTTCACTTCATTGTAGCCCCTACTGTTT
CACTTCATTGTAGCCCCTACTATTTCACCTCATTGTAGCCCCTACT
Found at i:1037092 original size:136 final size:136
Alignment explanation
Indices: 1036847--1037102 Score: 422
Period size: 136 Copynumber: 1.9 Consensus size: 136
1036837 TAAATATATA
* *
1036847 TAGCCCCTACTATTTCACTTCGTTGTAGCCCCAACTGTTTCACTTCGTTGTAGCCCTTACTATTT
1 TAGCCCCTACTATTTCACTTCGTTGTAGCCCCAACTATTTCACTTCGTTGTAGCCCCTACTATTT
* * *
1036912 CACTTTATTGTAGCCCCTACTTTTTCACTTCGTTGTAGCTCCTACTATTTCACTTTATTGTAGCC
66 CACTTCATTGTAGCCCCTACTTTTTCACCTCGTTGTAGCCCCTACTATTTCACTTTATTGTAGCC
1036977 CCTACT
131 CCTACT
* * * *
1036983 TAGCCCCTACTGTTTCACTTCGTTGTAGCCCCTACTATTTCACTTCGTTGTATCCCCTACTGTTT
1 TAGCCCCTACTATTTCACTTCGTTGTAGCCCCAACTATTTCACTTCGTTGTAGCCCCTACTATTT
*
1037048 CACTTCATTGTAGCCCCTACTTTTTCACCTCGTTGTAGCCCCTACTGTTTCACTT
66 CACTTCATTGTAGCCCCTACTTTTTCACCTCGTTGTAGCCCCTACTATTTCACTT
1037103 CGTTATGGGC
Statistics
Matches: 110, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
136 110 1.00
ACGTcount: A:0.16, C:0.32, G:0.11, T:0.41
Consensus pattern (136 bp):
TAGCCCCTACTATTTCACTTCGTTGTAGCCCCAACTATTTCACTTCGTTGTAGCCCCTACTATTT
CACTTCATTGTAGCCCCTACTTTTTCACCTCGTTGTAGCCCCTACTATTTCACTTTATTGTAGCC
CCTACT
Found at i:1037209 original size:25 final size:25
Alignment explanation
Indices: 1036983--1037198 Score: 290
Period size: 25 Copynumber: 8.6 Consensus size: 25
1036973 AGCCCCTACT
1036983 TAGCCCCTACTGTTTCACTTCGTTG
1 TAGCCCCTACTGTTTCACTTCGTTG
*
1037008 TAGCCCCTACTATTTCACTTCGTTG
1 TAGCCCCTACTGTTTCACTTCGTTG
* *
1037033 TATCCCCTACTGTTTCACTTCATTG
1 TAGCCCCTACTGTTTCACTTCGTTG
* *
1037058 TAGCCCCTACTTTTTCACCTCGTTG
1 TAGCCCCTACTGTTTCACTTCGTTG
*
1037083 TAGCCCCTACTGTTTCACTTCGTTA
1 TAGCCCCTACTGTTTCACTTCGTTG
* * *
1037108 TGGGCCCTACTGTTTCACTTCGTTA
1 TAGCCCCTACTGTTTCACTTCGTTG
* *
1037133 TGGGCCCTACTGTTTCACTTCGTTG
1 TAGCCCCTACTGTTTCACTTCGTTG
* *
1037158 TAGCCCGTATTAG-TTCACTTCGTTG
1 TAGCCCCTACT-GTTTCACTTCGTTG
*
1037183 TAGCCCCTACTATTTC
1 TAGCCCCTACTGTTTC
1037199 TTTTCATTGT
Statistics
Matches: 168, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
25 167 0.99
26 1 0.01
ACGTcount: A:0.14, C:0.31, G:0.15, T:0.40
Consensus pattern (25 bp):
TAGCCCCTACTGTTTCACTTCGTTG
Found at i:1037422 original size:30 final size:25
Alignment explanation
Indices: 1037306--1037402 Score: 113
Period size: 25 Copynumber: 3.7 Consensus size: 25
1037296 TTTATCAGTA
* * *
1037306 TCGTTGTAACCCCTACTATTTTAGT
1 TCGTTGTAGCCCCTACTATTTCACT
* *
1037331 TCGTTGTAGCCCCTATTTTTTTTCTCACT
1 TCGTTGTAGCCCCTA---CTATT-TCACT
1037360 TCGTTGTAGCCCCTACTATTTCACT
1 TCGTTGTAGCCCCTACTATTTCACT
1037385 TCGTTGTAGCCCCTACTA
1 TCGTTGTAGCCCCTACTA
1037403 ATCTATTTCA
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
25 37 0.61
26 3 0.05
28 3 0.05
29 18 0.30
ACGTcount: A:0.15, C:0.29, G:0.12, T:0.43
Consensus pattern (25 bp):
TCGTTGTAGCCCCTACTATTTCACT
Found at i:1038729 original size:2 final size:2
Alignment explanation
Indices: 1038722--1038748 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1038712 TAATGTTTCT
1038722 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1038749 TCTTCCTGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1040686 original size:12 final size:12
Alignment explanation
Indices: 1040671--1040695 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1040661 TGCATGTGAC
1040671 GCATATTGTTAT
1 GCATATTGTTAT
1040683 GCATATTGTTAT
1 GCATATTGTTAT
1040695 G
1 G
1040696 TAGGTTTCGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (12 bp):
GCATATTGTTAT
Found at i:1047206 original size:19 final size:19
Alignment explanation
Indices: 1047179--1047232 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
1047169 CACTTTTGAT
1047179 TTATATCCCATATGGGCTA
1 TTATATCCCATATGGGCTA
* * *
1047198 TTCTATCCCAAACGGGCTA
1 TTATATCCCATATGGGCTA
*
1047217 TTATATCCCATTTGGG
1 TTATATCCCATATGGG
1047233 AGATTGGTCC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (19 bp):
TTATATCCCATATGGGCTA
Found at i:1062719 original size:86 final size:86
Alignment explanation
Indices: 1062622--1062795 Score: 233
Period size: 86 Copynumber: 2.0 Consensus size: 86
1062612 ATTTGCTAAG
* ** * *
1062622 TTTGTGGTTTTCTTCCTCCATCTC-TTTCAGTTTGTTTTTTCCACAGTGGAAATCTGATTCTTCA
1 TTTGTCGTTTTCTTCCTCCATCTCTTTTCAGGGT-TTTTTTCCAAAGTAGAAATCTGATTCTTCA
*
1062686 AGTCTTTGTTCATGCTAGCAAT
65 AGTCTTTGTTCATACTAGCAAT
* * *
1062708 TTTGTCGTTTTCTTCCTCCATCTCTTTTGAGGGTTTTTTTCCAAAGTAGAAATTTGATTCTTCAT
1 TTTGTCGTTTTCTTCCTCCATCTCTTTTCAGGGTTTTTTTCCAAAGTAGAAATCTGATTCTTCAA
* *
1062773 GTCTTTTTTCATACTATCAAT
66 GTCTTTGTTCATACTAGCAAT
1062794 TT
1 TT
1062796 GTCCGGCTAT
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
86 70 0.92
87 6 0.08
ACGTcount: A:0.17, C:0.20, G:0.13, T:0.50
Consensus pattern (86 bp):
TTTGTCGTTTTCTTCCTCCATCTCTTTTCAGGGTTTTTTTCCAAAGTAGAAATCTGATTCTTCAA
GTCTTTGTTCATACTAGCAAT
Found at i:1065596 original size:42 final size:42
Alignment explanation
Indices: 1065550--1065665 Score: 130
Period size: 42 Copynumber: 2.7 Consensus size: 42
1065540 ACCTACTATG
*
1065550 TGCCTATACTGGACTTATCTTTTT-CATGGTGTACCTATAA-AA
1 TGCCTATGCTGGACTTATCTTTTTGCA--GTGTACCTATAAGAA
** *
1065592 TGCCTATGCTCTACTTAAACTTTTTGCAGTGTACCTATAAGAA
1 TGCCTATGCTGGACTT-ATCTTTTTGCAGTGTACCTATAAGAA
*
1065635 -ACCTATGCTGGACTTAGTCTTTTTGCAGTGT
1 TGCCTATGCTGGACTTA-TCTTTTTGCAGTGT
1065666 GCCTGAAATG
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
41 1 0.02
42 50 0.81
43 9 0.15
44 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (42 bp):
TGCCTATGCTGGACTTATCTTTTTGCAGTGTACCTATAAGAA
Found at i:1067282 original size:22 final size:22
Alignment explanation
Indices: 1067257--1067299 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1067247 AAACCAATTT
1067257 AATTCAGTCCATTTCAATGTAC
1 AATTCAGTCCATTTCAATGTAC
*
1067279 AATTCAGTCCATTTCGATGTA
1 AATTCAGTCCATTTCAATGTA
1067300 TAAACTTGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (22 bp):
AATTCAGTCCATTTCAATGTAC
Found at i:1072082 original size:2 final size:2
Alignment explanation
Indices: 1072075--1072109 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1072065 AAAATAGTAC
1072075 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1072110 ATTTATGTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1083359 original size:381 final size:377
Alignment explanation
Indices: 1082614--1083360 Score: 1377
Period size: 381 Copynumber: 2.0 Consensus size: 377
1082604 TGTCTAATAG
* *
1082614 ATTGCAAGTTTGATCTCTAAAATCTTTGTGTGATTTTAATGGGTTTATTGATTAATAAAGATTCC
1 ATTGCAAGTTTGATCACTAAAATCTTTGTGTGATTTTAATGGATTTATTGATTAATAAAGATTCC
*
1082679 CCTCTGAAATTCAAAAAAAAAAAATTAAAAATTTATCATATATGTTAAAGTTTACATTGAGGTTG
66 CCTCTGAAATTCAAAAAAAAAAAATGAAAAATTTATCATATATGTTAAAGTTTACATTGAGGTTG
1082744 ATGGGGAAAATGCATTAATATATTGTTTAAGTACAAGTAATTTTCTCACATTTTTCTTTGTGGAA
131 ATGGGGAAAATGCATTAATATATTGTTTAAGTACAAGTAATTTTCTCACATTTTTCTTTGTGGAA
* *
1082809 CATTGCAAAATGAAGCTTCTCCTTTCTTCAAATATGCTAAAATAATTCATGATTTACCATTCATA
196 CATTGCAAAACGAAGCTTCTCCTTTCTTCAAATATGCTAAAATAATTCATGACTTACCATTCATA
1082874 ATTTCATAAATTTTTAATAAATTCGTAAAGGGCTGACAACTCTTTAAAAAAAGTTTTAAGTGCAA
261 ATTTCATAAATTTTTAATAAATTCGTAAAGGGCTGACAACTCTTTAAAAAAAGTTTTAAGTGCAA
1082939 AAAGTTCATTAAATGAACTACATAGTATACATAACCCCCCGAGTTTGGTTTA
326 AAAGTTCATTAAATGAACTACATAGTATACATAACCCCCCGAGTTTGGTTTA
1082991 NATTGCAAGTTTGATCACTAAAATCTTTGTGTGATTTTAATGGATTTATTGATTAATAAAGATTC
1 -ATTGCAAGTTTGATCACTAAAATCTTTGTGTGATTTTAATGGATTTATTGATTAATAAAGATTC
* *
1083056 CCCTCTGAAATTCCAACACAAAAAAAATGAACAAATTTATCATATATGTTAAAGTTTAGATTGAG
65 CCCTCTGAAATT-CAA-AAAAAAAAAATGAA-AAATTTATCATATATGTTAAAGTTTACATTGAG
1083121 GTTGATGGGGAAAATGCATTAATATATTGTTTAAGTACAAGTAATTTTCTCACATTTTTCTTTGT
127 GTTGATGGGGAAAATGCATTAATATATTGTTTAAGTACAAGTAATTTTCTCACATTTTTCTTTGT
1083186 GGAACATTGCAAAACGAAGCTTCTCCTTTCTTCAAATATGCTAAAATAATTCATGACTTACCATT
192 GGAACATTGCAAAACGAAGCTTCTCCTTTCTTCAAATATGCTAAAATAATTCATGACTTACCATT
1083251 CATAATTTCATAAATTTTTAATAAATTCGTAAAGGGCTGACAACTCTTTAAAAAAAAGTTTTAAG
257 CATAATTTCATAAATTTTTAATAAATTCGTAAAGGGCTGACAACTCTTT-AAAAAAAGTTTTAAG
*
1083316 TGCAAAAAGTTCATTAAATGAACTACATAGTATACATACCCCCCC
321 TGCAAAAAGTTCATTAAATGAACTACATAGTATACATAACCCCCC
1083361 CCCCCCCATG
Statistics
Matches: 357, Mismatches: 8, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
378 74 0.21
379 3 0.01
380 12 0.03
381 209 0.59
382 59 0.17
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (377 bp):
ATTGCAAGTTTGATCACTAAAATCTTTGTGTGATTTTAATGGATTTATTGATTAATAAAGATTCC
CCTCTGAAATTCAAAAAAAAAAAATGAAAAATTTATCATATATGTTAAAGTTTACATTGAGGTTG
ATGGGGAAAATGCATTAATATATTGTTTAAGTACAAGTAATTTTCTCACATTTTTCTTTGTGGAA
CATTGCAAAACGAAGCTTCTCCTTTCTTCAAATATGCTAAAATAATTCATGACTTACCATTCATA
ATTTCATAAATTTTTAATAAATTCGTAAAGGGCTGACAACTCTTTAAAAAAAGTTTTAAGTGCAA
AAAGTTCATTAAATGAACTACATAGTATACATAACCCCCCGAGTTTGGTTTA
Found at i:1088630 original size:1 final size:1
Alignment explanation
Indices: 1088624--1088665 Score: 84
Period size: 1 Copynumber: 42.0 Consensus size: 1
1088614 CAGCACATAA
1088624 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1088666 GCATCAGCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1098645 original size:166 final size:165
Alignment explanation
Indices: 1098371--1098990 Score: 933
Period size: 166 Copynumber: 3.8 Consensus size: 165
1098361 CCATAAGACC
* * * * *
1098371 AGGAAAGCTGAAACTTGTGTGGAAGCAACCTCAGGTAGTGTAGATACAAAATTGTGAAATTCATG
1 AGGAAAGCTGAAACTTGTGTTGAAGCATCCTCAGGTAGTGTAAATTCAAAATTGTGAAAATCATG
* * *
1098436 ACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGATCGAAGTTTAACATATGATTATATAGAGTAT
66 ACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGATCGAAGTTTAACATAGGAATATATAGAGTAA
** *
1098501 ATCTTTAAAAATCTTCTCCACAGAAACTAATCTTCT
131 ATCTTTAAAAATCTTCTCC-CAGAAACTAATCAGCA
* *
1098537 AGGAAAGCTGACACTTGTGTTGAAGCATCCTCAGGTAGTGTAAATTCAAAGTTGTGAAAATCATG
1 AGGAAAGCTGAAACTTGTGTTGAAGCATCCTCAGGTAGTGTAAATTCAAAATTGTGAAAATCATG
* *
1098602 ACCCCCGGGGGTAGGCTGGGGCCACAATGAGGGG-TCGAAGTTTAACATATGAATATATAGAGTA
66 ACCCCCGGGGGTAGGGTGGGGCCACAATG-GGGGATCGAAGTTTAACATAGGAATATATAGAGTA
* *
1098666 AATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCC
130 AATCTTTAAAAATCTTC-TCCCAGAAACTAATCAGCA
1098703 AGGAAAGCTGAAACTTGTGTTGAAGCATCCTCAGGTAGTGTAAATTCAAAATTGTGAAAATCATG
1 AGGAAAGCTGAAACTTGTGTTGAAGCATCCTCAGGTAGTGTAAATTCAAAATTGTGAAAATCATG
* * * * *
1098768 ATCCCCGGGGGTAGGGTGGGGCCAAAATAGGGGGGTCGAAGTTTTACATAGGAATATATATAGTA
66 ACCCCCGGGGGTAGGGTGGGGCCACAAT-GGGGGATCGAAGTTTAACATAGGAATATATAGAGTA
*
1098833 AATCTTTAAAACTC-T-TCCCAGAAACTAATCAGCA
130 AATCTTTAAAAATCTTCTCCCAGAAACTAATCAGCA
* *
1098867 AGGAAAGCTGAAACTTGT-ATGAAAGCATCCTCAGGTAGTGTAAATTCAAAGTTGTGAAAATCAT
1 AGGAAAGCTGAAACTTGTGTTG-AAGCATCCTCAGGTAGTGTAAATTCAAAATTGTGAAAATCAT
*
1098931 GACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGATCGAAGTTTTACATAGGAATATATA
65 GACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGATCGAAGTTTAACATAGGAATATATA
1098991 TANNNNNNNN
Statistics
Matches: 419, Mismatches: 30, Indels: 13
0.91 0.06 0.03
Matches are distributed among these distances:
163 32 0.08
164 103 0.25
166 237 0.57
167 47 0.11
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (165 bp):
AGGAAAGCTGAAACTTGTGTTGAAGCATCCTCAGGTAGTGTAAATTCAAAATTGTGAAAATCATG
ACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGATCGAAGTTTAACATAGGAATATATAGAGTAA
ATCTTTAAAAATCTTCTCCCAGAAACTAATCAGCA
Found at i:1098954 original size:330 final size:332
Alignment explanation
Indices: 1098369--1098990 Score: 984
Period size: 330 Copynumber: 1.9 Consensus size: 332
1098359 AACCATAAGA
* *
1098369 CCAGGAAAGCTGAAACTTGTGTGGAAGCAACCTCAGGTAGTGTAGATACAAAATTGTGAAATTCA
1 CCAGGAAAGCTGAAACTTGTGTGGAAGCAACCTCAGGTAGTGTAAATACAAAATTGTGAAAATCA
* * *
1098434 TGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGATCGAAGTTTAACATATGATTATATAGAGT
66 TGACCCCCGGGGGTAGGGTGGGGCCAAAATGGGGGATCGAAGTTTAACATAGGAATATATAGAGT
* ** * * *
1098499 ATATCTTTAAAAATCTTCTCCACAGAAACTAATCTTCTAGGAAAGCTGACACTTGTGTTGAAGCA
131 AAATCTTTAAAAATCTTCTCCACAGAAACTAATCAGCAAGGAAAGCTGAAACTTGTGATGAAGCA
1098564 TCCTCAGGTAGTGTAAATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGCTGGGGCCACAA
196 TCCTCAGGTAGTGTAAATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGCTGGGGCCACAA
*
1098629 TGAGGGG-TCGAAGTTTAACATATGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAA
261 TG-GGGGATCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAA
1098693 CTAATCAG
325 CTAATCAG
* * *
1098701 CCAGGAAAGCTGAAACTTGTGTTGAAGCATCCTCAGGTAGTGTAAATTCAAAATTGTGAAAATCA
1 CCAGGAAAGCTGAAACTTGTGTGGAAGCAACCTCAGGTAGTGTAAATACAAAATTGTGAAAATCA
* * * *
1098766 TGATCCCCGGGGGTAGGGTGGGGCCAAAATAGGGGGGTCGAAGTTTTACATAGGAATATATATAG
66 TGACCCCCGGGGGTAGGGTGGGGCCAAAAT-GGGGGATCGAAGTTTAACATAGGAATATATAGAG
*
1098831 TAAATCTTTAAAACTC-T-TCC-CAGAAACTAATCAGCAAGGAAAGCTGAAACTTGT-ATGAAAG
130 TAAATCTTTAAAAATCTTCTCCACAGAAACTAATCAGCAAGGAAAGCTGAAACTTGTGATG-AAG
*
1098892 CATCCTCAGGTAGTGTAAATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCAC
194 CATCCTCAGGTAGTGTAAATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGCTGGGGCCAC
*
1098957 AATGGGGGATCGAAGTTTTACATAGGAATATATA
259 AATGGGGGATCGAAGTTTAACATAGGAATATATA
1098991 TANNNNNNNN
Statistics
Matches: 265, Mismatches: 22, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
329 6 0.02
330 124 0.47
331 3 0.01
332 89 0.34
333 43 0.16
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.25
Consensus pattern (332 bp):
CCAGGAAAGCTGAAACTTGTGTGGAAGCAACCTCAGGTAGTGTAAATACAAAATTGTGAAAATCA
TGACCCCCGGGGGTAGGGTGGGGCCAAAATGGGGGATCGAAGTTTAACATAGGAATATATAGAGT
AAATCTTTAAAAATCTTCTCCACAGAAACTAATCAGCAAGGAAAGCTGAAACTTGTGATGAAGCA
TCCTCAGGTAGTGTAAATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGCTGGGGCCACAA
TGGGGGATCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAAC
TAATCAG
Found at i:1104829 original size:2 final size:2
Alignment explanation
Indices: 1104822--1104887 Score: 123
Period size: 2 Copynumber: 33.0 Consensus size: 2
1104812 GCTCTTTAGA
*
1104822 AG AG AG AG AG AG AG AG TG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1104864 AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG
1104888 GGGCGTGTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.48, C:0.00, G:0.50, T:0.02
Consensus pattern (2 bp):
AG
Found at i:1105067 original size:3 final size:3
Alignment explanation
Indices: 1105059--1105093 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
1105049 GTTTCACAAT
* *
1105059 TAA TAA TAA TAA TTA TTA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1105094 TGTAGCTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:1117116 original size:16 final size:17
Alignment explanation
Indices: 1117090--1117121 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1117080 TGGGAAAATG
1117090 AGCACAGAGAGAGAGAA
1 AGCACAGAGAGAGAGAA
1117107 AGCA-AGAGAGAGAGA
1 AGCACAGAGAGAGAGA
1117122 GAGAGTTGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.53, C:0.09, G:0.38, T:0.00
Consensus pattern (17 bp):
AGCACAGAGAGAGAGAA
Found at i:1122317 original size:32 final size:32
Alignment explanation
Indices: 1122274--1122389 Score: 141
Period size: 32 Copynumber: 3.8 Consensus size: 32
1122264 CCATGTCCCT
* *
1122274 TTAACAATACACACATTTTTCAGACATGGAAC
1 TTAACAATACACACATATTTCAGACAAGGAAC
*
1122306 TTAACATTACACACATATTTCAGACAAGG-A-
1 TTAACAATACACACATATTTCAGACAAGGAAC
* ** *
1122336 --AACAATTCACATTTATTTCAGATAAGGAAC
1 TTAACAATACACACATATTTCAGACAAGGAAC
1122366 TTAACAATACACACATATTTCAGA
1 TTAACAATACACACATATTTCAGA
1122390 AAACAATACA
Statistics
Matches: 69, Mismatches: 11, Indels: 8
0.78 0.12 0.09
Matches are distributed among these distances:
28 22 0.32
29 1 0.01
31 1 0.01
32 45 0.65
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.28
Consensus pattern (32 bp):
TTAACAATACACACATATTTCAGACAAGGAAC
Found at i:1122398 original size:23 final size:23
Alignment explanation
Indices: 1122368--1122412 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1122358 TAAGGAACTT
1122368 AACAATACACACATATTTCAGAA
1 AACAATACACACATATTTCAGAA
**
1122391 AACAATACACATTTATTTCAGA
1 AACAATACACACATATTTCAGA
1122413 CAAGGAAGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.49, C:0.20, G:0.04, T:0.27
Consensus pattern (23 bp):
AACAATACACACATATTTCAGAA
Found at i:1122419 original size:55 final size:57
Alignment explanation
Indices: 1122276--1122419 Score: 186
Period size: 60 Copynumber: 2.5 Consensus size: 57
1122266 ATGTCCCTTT
* * *
1122276 AACAATACACACATT-TTTCAGACATGGAACTTAACATTACACACATATTTCAGACAAGGA
1 AACAATACACA-TTTATTTCAGACAAGGAACTTAACAATACACACATATTTCAG--AA-GA
* *
1122336 AACAATTCACATTTATTTCAGATAAGGAACTTAACAATACACACATATTTCAG-A-A
1 AACAATACACATTTATTTCAGACAAGGAACTTAACAATACACACATATTTCAGAAGA
1122391 AACAATACACATTTATTTCAGACAAGGAA
1 AACAATACACATTTATTTCAGACAAGGAA
1122420 GCTATACAAG
Statistics
Matches: 76, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
55 28 0.37
57 1 0.01
59 2 0.03
60 45 0.59
ACGTcount: A:0.45, C:0.19, G:0.09, T:0.26
Consensus pattern (57 bp):
AACAATACACATTTATTTCAGACAAGGAACTTAACAATACACACATATTTCAGAAGA
Found at i:1127052 original size:2 final size:2
Alignment explanation
Indices: 1127045--1127081 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
1127035 TTGATCTCAA
*
1127045 AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G GG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1127082 TGCATCATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1131498 original size:238 final size:237
Alignment explanation
Indices: 1131080--1131554 Score: 941
Period size: 238 Copynumber: 2.0 Consensus size: 237
1131070 TTTGATATTT
1131080 ATTATTTAATGGCATTACCATGTTCTGTACCTCGTCGCTAAAAAAGTAGCTATTTACATTAGTTG
1 ATTATTTAATGGCATTACCATGTTCTGTACCTCGTCGCTAAAAAAGTAGCTATTTACATTAGTTG
1131145 TCCCATATGAATCTGATTGAAATCCACTCTTTTTAAAAGAGCTTCAGTGTTATGTTGTTCAGTAA
66 TCCCATATGAATCTGATTGAAATCCACTCTTTTTAAAAGAGCTTCAGTGTTATGTTGTTCAGTAA
1131210 TTCTTTTTCTTTAGTTTTTATATACTTATATATATATATATTAGTTGGTTTATTTCTTGTTGTGA
131 TTCTTTTTCTTTAGTTTTTATATACTTATATATATATATATTAGTTGGTTTATTTCTTGTTGTGA
1131275 CTTGGTCTCGGCTGTAGTTCAGTGTTGTTGTGGCTTTGTACA
196 CTTGGTCTCGGCTGTAGTTCAGTGTTGTTGTGGCTTTGTACA
1131317 NATTATTTAATGGCATTACCATGTTCTGTACCTCGTCGCTAAAAAAGTAGCTATTTACATTAGTT
1 -ATTATTTAATGGCATTACCATGTTCTGTACCTCGTCGCTAAAAAAGTAGCTATTTACATTAGTT
1131382 GTCCCATATGAATCTGATTGAAATCCACTCTTTTTAAAAGAGCTTCAGTGTTATGTTGTTCAGTA
65 GTCCCATATGAATCTGATTGAAATCCACTCTTTTTAAAAGAGCTTCAGTGTTATGTTGTTCAGTA
1131447 ATTCTTTTTCTTTAGTTTTTATATACTTATATATATATATATTAGTTGGTTTATTTCTTGTTGTG
130 ATTCTTTTTCTTTAGTTTTTATATACTTATATATATATATATTAGTTGGTTTATTTCTTGTTGTG
1131512 ACTTGGTCTCGGCTGTAGTTCAGTGTTGTTGTGGCTTTGTACA
195 ACTTGGTCTCGGCTGTAGTTCAGTGTTGTTGTGGCTTTGTACA
1131555 GGCGTACACA
Statistics
Matches: 237, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
238 237 1.00
ACGTcount: A:0.24, C:0.14, G:0.17, T:0.45
Consensus pattern (237 bp):
ATTATTTAATGGCATTACCATGTTCTGTACCTCGTCGCTAAAAAAGTAGCTATTTACATTAGTTG
TCCCATATGAATCTGATTGAAATCCACTCTTTTTAAAAGAGCTTCAGTGTTATGTTGTTCAGTAA
TTCTTTTTCTTTAGTTTTTATATACTTATATATATATATATTAGTTGGTTTATTTCTTGTTGTGA
CTTGGTCTCGGCTGTAGTTCAGTGTTGTTGTGGCTTTGTACA
Found at i:1134705 original size:31 final size:31
Alignment explanation
Indices: 1134668--1134862 Score: 291
Period size: 31 Copynumber: 6.3 Consensus size: 31
1134658 TTGTGAAATN
*
1134668 AAATCAATTCAAGTTAAATCTAACAAACTTG
1 AAATCAATTCAAGTTAAATCTAACAACCTTG
*
1134699 AAATCAATTCAAGTTCAATCTAACAACCTTG
1 AAATCAATTCAAGTTAAATCTAACAACCTTG
* ** *
1134730 AAATCAATTCAAGTTTAATCTAACTGCTTTG
1 AAATCAATTCAAGTTAAATCTAACAACCTTG
1134761 AAATCAATTTCAAGTTAAATCTAACAACCTTG
1 AAATCAA-TTCAAGTTAAATCTAACAACCTTG
*
1134793 AAATCAATTCAAGTTAAATCTAACAACCCTG
1 AAATCAATTCAAGTTAAATCTAACAACCTTG
* * *
1134824 AAATCAATTCAGGTTGAATATAACAACCTTG
1 AAATCAATTCAAGTTAAATCTAACAACCTTG
1134855 AAATCAAT
1 AAATCAAT
1134863 ACAATTCATT
Statistics
Matches: 148, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
31 121 0.82
32 27 0.18
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.30
Consensus pattern (31 bp):
AAATCAATTCAAGTTAAATCTAACAACCTTG
Found at i:1134779 original size:94 final size:94
Alignment explanation
Indices: 1134668--1134862 Score: 302
Period size: 94 Copynumber: 2.1 Consensus size: 94
1134658 TTGTGAAATN
* *
1134668 AAATCAA-TTCAAGTTAAATCTAACAAACTTGAAATCAATTCAAGTTCAATCTAACAACCTTGAA
1 AAATCAATTTCAAGTTAAATCTAACAAACTTGAAATCAATTCAAGTTAAATCTAACAACCCTGAA
* * ** *
1134732 ATCAATTCAAGTTTAATCTAACTGCTTTG
66 ATCAATTCAAGTTGAATATAACAACCTTG
*
1134761 AAATCAATTTCAAGTTAAATCTAACAACCTTGAAATCAATTCAAGTTAAATCTAACAACCCTGAA
1 AAATCAATTTCAAGTTAAATCTAACAAACTTGAAATCAATTCAAGTTAAATCTAACAACCCTGAA
*
1134826 ATCAATTCAGGTTGAATATAACAACCTTG
66 ATCAATTCAAGTTGAATATAACAACCTTG
1134855 AAATCAAT
1 AAATCAAT
1134863 ACAATTCATT
Statistics
Matches: 92, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
93 7 0.08
94 85 0.92
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.30
Consensus pattern (94 bp):
AAATCAATTTCAAGTTAAATCTAACAAACTTGAAATCAATTCAAGTTAAATCTAACAACCCTGAA
ATCAATTCAAGTTGAATATAACAACCTTG
Found at i:1135171 original size:22 final size:21
Alignment explanation
Indices: 1135139--1135180 Score: 75
Period size: 22 Copynumber: 2.0 Consensus size: 21
1135129 CAAGAAGCTA
1135139 CAAAAAAACAAAAACAAAACC
1 CAAAAAAACAAAAACAAAACC
1135160 CAAAACAAACAAAAACAAAAC
1 CAAAA-AAACAAAAACAAAAC
1135181 AACATCAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.76, C:0.24, G:0.00, T:0.00
Consensus pattern (21 bp):
CAAAAAAACAAAAACAAAACC
Found at i:1137066 original size:85 final size:85
Alignment explanation
Indices: 1136771--1137225 Score: 531
Period size: 85 Copynumber: 5.3 Consensus size: 85
1136761 GTTTGTATCT
***
1136771 TACACATATTTGAAAGTATCATACACATATTTAATCGCGTATCATACACATTTTCCTCTACCATA
1 TACACATATTTGCCCGTATCATACACATATTTAATCGCGTATCATACACATTTTCCTCTACCATA
1136836 CACATATCTGTTGCGTATAC
66 CACATATCTGTTGCGTATAC
* * * * *
1136856 TACACATATTAGCCCGTATCATTCACATATTTAATCGCGTGTCATACACATTTTCTTCGTATCAT
1 TACACATATTTGCCCGTATCATACACATATTTAATCGCGTATCATACACATTTTCCTC-TACCAT
**
1136921 ACACATATCTGTTCGCGTATTT
65 ACACATATCTGTT-GCGTATAC
* * **
1136943 TTCACATATTTGCCCGTATCATGCACATATTTCTTCGCGTATCATACACATTTTCCTCTACCATA
1 TACACATATTTGCCCGTATCATACACATATTTAATCGCGTATCATACACATTTTCCTCTACCATA
*
1137008 CACATATCTGTTGCATATAC
66 CACATATCTGTTGCGTATAC
* * * * *
1137028 TACACATATTTGCCCGTATCATACAAATATTAAATCGCGTATCATACACATTTTCTTCGCATCAT
1 TACACATATTTGCCCGTATCATACACATATTTAATCGCGTATCATACACATTTTCCTC-TACCAT
**
1137093 ACACATAATTATCTGTTCGCGTATTT
65 ACAC---A-TATCTGTT-GCGTATAC
* * ** * * *
1137119 TACACATATTTGCCTGTATCATGCACATATTTGTTCGTGTATCATACATATTTT-C-CT--CGTA
1 TACACATATTTGCCCGTATCATACACATATTTAATCGCGTATCATACACATTTTCCTCTACCATA
*
1137180 CACATATTTGTTTGCGTATAC
66 CACATATCTG-TTGCGTATAC
1137201 TACACATATTTGCCCGTATCATACA
1 TACACATATTTGCCCGTATCATACA
1137226 TGTACATATA
Statistics
Matches: 312, Mismatches: 49, Indels: 21
0.82 0.13 0.05
Matches are distributed among these distances:
82 34 0.11
83 3 0.01
85 107 0.34
86 50 0.16
87 57 0.18
89 2 0.01
90 8 0.03
91 51 0.16
ACGTcount: A:0.28, C:0.24, G:0.09, T:0.38
Consensus pattern (85 bp):
TACACATATTTGCCCGTATCATACACATATTTAATCGCGTATCATACACATTTTCCTCTACCATA
CACATATCTGTTGCGTATAC
Found at i:1137066 original size:172 final size:174
Alignment explanation
Indices: 1136765--1137225 Score: 664
Period size: 172 Copynumber: 2.7 Consensus size: 174
1136755 CAACTTGTTT
* *** * *
1136765 GTATCTTACACATATTTGAAAGTATCATACACATATTTAATCGCGTATCATACACATTTTCCTCT
1 GTATTTTACACATATTTGCCCGTATCATGCACATATTTATTCGCGTATCATACACATTTTCCTCT
* * * *
1136830 ACCATACACATATCTGTTGCGTATACTACACATATTAGCCCGTATCATTCACATATTTAATCGCG
66 ACCATACACATATCTGTTGCGTATACTACACATATTTGCCCGTATCATACAAATATTAAATCGCG
* *
1136895 TGTCATACACATTTTCTTCGTATCATACAC-A-TATCTGTTCGC
131 TATCATACACATTTTCTTCGCATCATACACAATTATCTGTTCGC
* *
1136937 GTATTTTTCACATATTTGCCCGTATCATGCACATATTTCTTCGCGTATCATACACATTTTCCTCT
1 GTATTTTACACATATTTGCCCGTATCATGCACATATTTATTCGCGTATCATACACATTTTCCTCT
*
1137002 ACCATACACATATCTGTTGCATATACTACACATATTTGCCCGTATCATACAAATATTAAATCGCG
66 ACCATACACATATCTGTTGCGTATACTACACATATTTGCCCGTATCATACAAATATTAAATCGCG
1137067 TATCATACACATTTTCTTCGCATCATACACATAATTATCTGTTCGC
131 TATCATACACATTTTCTTCGCATCATACAC--AATTATCTGTTCGC
* * * *
1137113 GTATTTTACACATATTTGCCTGTATCATGCACATATTTGTTCGTGTATCATACATATTTT-C-CT
1 GTATTTTACACATATTTGCCCGTATCATGCACATATTTATTCGCGTATCATACACATTTTCCTCT
* *
1137176 --CGTACACATATTTGTTTGCGTATACTACACATATTTGCCCGTATCATACA
66 ACCATACACATATCTG-TTGCGTATACTACACATATTTGCCCGTATCATACA
1137226 TGTACATATA
Statistics
Matches: 261, Mismatches: 23, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
172 157 0.60
173 34 0.13
174 2 0.01
175 2 0.01
176 66 0.25
ACGTcount: A:0.28, C:0.24, G:0.10, T:0.38
Consensus pattern (174 bp):
GTATTTTACACATATTTGCCCGTATCATGCACATATTTATTCGCGTATCATACACATTTTCCTCT
ACCATACACATATCTGTTGCGTATACTACACATATTTGCCCGTATCATACAAATATTAAATCGCG
TATCATACACATTTTCTTCGCATCATACACAATTATCTGTTCGC
Found at i:1137163 original size:23 final size:20
Alignment explanation
Indices: 1137121--1137171 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
1137111 GCGTATTTTA
1137121 CACATATTTGCCTGTATCAT
1 CACATATTTGCCTGTATCAT
*
1137141 GCACATATTTGTTCGTGTATCAT
1 -CACATATTTG--CCTGTATCAT
1137164 -ACATATTT
1 CACATATTT
1137172 TCCTCGTACA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 18 0.67
23 9 0.33
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.43
Consensus pattern (20 bp):
CACATATTTGCCTGTATCAT
Found at i:1137259 original size:23 final size:23
Alignment explanation
Indices: 1137228--1137280 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
1137218 ATCATACATG
* * * *
1137228 TACATATATTTATTCGTGTATCA
1 TACACATATTTAATCGCGCATCA
1137251 TACACATATTTAATCGCGCATCA
1 TACACATATTTAATCGCGCATCA
1137274 TACACAT
1 TACACAT
1137281 TTTCCTCGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.38
Consensus pattern (23 bp):
TACACATATTTAATCGCGCATCA
Found at i:1139354 original size:18 final size:18
Alignment explanation
Indices: 1139331--1139426 Score: 63
Period size: 18 Copynumber: 5.2 Consensus size: 18
1139321 AACACAAACC
1139331 ACAATACAACACAACATA
1 ACAATACAACACAACATA
*
1139349 ACAATACAATACAACA-A
1 ACAATACAACACAACATA
*
1139366 TACACTACAATAGCACAACATA
1 -ACAATAC-A-A-CACAACATA
* * *
1139388 ACTAA-ATAGCACAACAAA
1 AC-AATACAACACAACATA
*
1139406 ACAAATA-AACACAACACA
1 AC-AATACAACACAACATA
1139424 ACA
1 ACA
1139427 CCGCACTACA
Statistics
Matches: 61, Mismatches: 10, Indels: 15
0.71 0.12 0.17
Matches are distributed among these distances:
17 2 0.03
18 44 0.72
19 2 0.03
20 2 0.03
21 9 0.15
22 2 0.03
ACGTcount: A:0.60, C:0.26, G:0.02, T:0.11
Consensus pattern (18 bp):
ACAATACAACACAACATA
Found at i:1139383 original size:21 final size:19
Alignment explanation
Indices: 1139359--1139412 Score: 69
Period size: 18 Copynumber: 2.9 Consensus size: 19
1139349 ACAATACAAT
1139359 ACAACAATACACTACAATAGC
1 ACAACAATA-ACTA-AATAGC
1139380 ACAAC-ATAACTAAATAGC
1 ACAACAATAACTAAATAGC
1139398 ACAACAA-AAC-AAATA
1 ACAACAATAACTAAATA
1139413 AACACAACAC
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
17 5 0.16
18 14 0.44
19 5 0.16
20 3 0.09
21 5 0.16
ACGTcount: A:0.59, C:0.24, G:0.04, T:0.13
Consensus pattern (19 bp):
ACAACAATAACTAAATAGC
Found at i:1139446 original size:21 final size:21
Alignment explanation
Indices: 1139367--1139523 Score: 68
Period size: 21 Copynumber: 7.1 Consensus size: 21
1139357 ATACAACAAT
* *
1139367 ACACTACAATAGCACAACA-T
1 ACACTACAACAGCACAACACA
* *
1139387 A-ACTA-AATAGCACAACAAA
1 ACACTACAACAGCACAACACA
* * * *
1139406 ACAAATAAACACAACACAACACC
1 AC-ACTACA-ACAGCACAACACA
*
1139429 GCACTACAACAGCACAACACA
1 ACACTACAACAGCACAACACA
* * *
1139450 ACACTACAACATAACATCACAAAAA
1 ACACTACAAC--AGCA-CA-ACACA
*
1139475 CACTACACTACAACAGCACAACATA
1 -AC-AC--TACAACAGCACAACACA
* *
1139500 GCACTACAACAGCACAACATA
1 ACACTACAACAGCACAACACA
1139521 ACA
1 ACA
1139524 AAACAGCACA
Statistics
Matches: 104, Mismatches: 20, Indels: 25
0.70 0.13 0.17
Matches are distributed among these distances:
18 12 0.12
19 5 0.05
20 1 0.01
21 42 0.40
22 5 0.05
23 15 0.14
24 3 0.03
25 6 0.06
26 4 0.04
27 5 0.05
29 6 0.06
ACGTcount: A:0.54, C:0.32, G:0.04, T:0.10
Consensus pattern (21 bp):
ACACTACAACAGCACAACACA
Found at i:1139450 original size:13 final size:12
Alignment explanation
Indices: 1139414--1139497 Score: 50
Period size: 13 Copynumber: 6.7 Consensus size: 12
1139404 AAACAAATAA
1139414 ACACAACACAAC
1 ACACAACACAAC
*
1139426 AC-CGCACTACAAC
1 ACAC-AAC-ACAAC
1139439 AGCACAACACAAC
1 A-CACAACACAAC
*
1139452 ACTACAACATAAC
1 AC-ACAACACAAC
1139465 ATCACAA-A-AAC
1 A-CACAACACAAC
1139476 ACTAC-ACTACAAC
1 AC-ACAAC-ACAAC
1139489 AGCACAACA
1 A-CACAACA
1139498 TAGCACTACA
Statistics
Matches: 57, Mismatches: 3, Indels: 23
0.69 0.04 0.28
Matches are distributed among these distances:
10 2 0.04
11 7 0.12
12 7 0.12
13 33 0.58
14 7 0.12
15 1 0.02
ACGTcount: A:0.52, C:0.37, G:0.04, T:0.07
Consensus pattern (12 bp):
ACACAACACAAC
Found at i:1139530 original size:18 final size:18
Alignment explanation
Indices: 1139484--1139552 Score: 86
Period size: 18 Copynumber: 3.7 Consensus size: 18
1139474 ACACTACACT
1139484 ACAACAGCACAACATAGCAC
1 ACAACAGCACAACATA--AC
1139504 TACAACAGCACAACATAAC
1 -ACAACAGCACAACATAAC
*
1139523 AAAACAGCAC-ACTATAAC
1 ACAACAGCACAAC-ATAAC
1139541 ACAACAGCACAA
1 ACAACAGCACAA
1139553 TACACGACGT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
17 2 0.05
18 23 0.52
19 3 0.07
21 16 0.36
ACGTcount: A:0.54, C:0.32, G:0.07, T:0.07
Consensus pattern (18 bp):
ACAACAGCACAACATAAC
Found at i:1143258 original size:2 final size:2
Alignment explanation
Indices: 1143251--1143320 Score: 119
Period size: 2 Copynumber: 36.5 Consensus size: 2
1143241 TCTTATCTTT
1143251 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1143292 TA TA TA -A TA TA TA -A TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1143321 GTATCGTGCT
Statistics
Matches: 65, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
1 3 0.05
2 62 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1151894 original size:43 final size:43
Alignment explanation
Indices: 1151832--1152111 Score: 323
Period size: 43 Copynumber: 6.4 Consensus size: 43
1151822 CATCCCTTTA
* *
1151832 CCACCTGTAGGCAGTTTAGAGGAATGATGGGATATAACGAGTC
1 CCACCTGTAAGCAGGTTAGAGGAATGATGGGATATAACGAGTC
* ***
1151875 CCACCTGTAAGCAGGTTAGAGGAATTATGGGATACCGCGAGTC
1 CCACCTGTAAGCAGGTTAGAGGAATGATGGGATATAACGAGTC
**
1151918 ATACCTGT-AGTCAGGTTAGAGGAATGATGGGATATAACGAGTC
1 CCACCTGTAAG-CAGGTTAGAGGAATGATGGGATATAACGAGTC
1151961 CCACCTGT-AGTCAGGTTAGAGGAATGATGGGATATAACGAGTC
1 CCACCTGTAAG-CAGGTTAGAGGAATGATGGGATATAACGAGTC
* ***
1152004 CCACCTAGCTGTAAGCAGGTTAGAGGAATTATGGGATACCGCGAGTC
1 CCA-C---CTGTAAGCAGGTTAGAGGAATGATGGGATATAACGAGTC
**
1152051 ATACCTGT-AGTCAGGTTAGAGGAATGATGGGATATAACGAGTC
1 CCACCTGTAAG-CAGGTTAGAGGAATGATGGGATATAACGAGTC
* * *
1152094 CTACCTGTAGGCAAGTTA
1 CCACCTGTAAGCAGGTTA
1152112 AAGCAACATT
Statistics
Matches: 202, Mismatches: 27, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
42 4 0.02
43 160 0.79
44 2 0.01
46 1 0.00
47 33 0.16
48 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.24
Consensus pattern (43 bp):
CCACCTGTAAGCAGGTTAGAGGAATGATGGGATATAACGAGTC
Found at i:1152057 original size:90 final size:90
Alignment explanation
Indices: 1151834--1152099 Score: 346
Period size: 90 Copynumber: 3.0 Consensus size: 90
1151824 TCCCTTTACC
* *
1151834 ACCTGTAGGCAGTTTAGAGGAATGATGGGATATAACGAGTCCCACCTGTAAG-CAGGTTAGAGGA
1 ACCTGTAAGCAGGTTAGAGGAATGATGGGATATAACGAGTCCCACCTGT-AGTCAGGTTAGAGGA
* ***
1151898 ATTATGGGATACCGCGAGT--CA--T
65 ATGATGGGATATAACGAGTCCCACCT
1151920 ACCTGT-AGTCAGGTTAGAGGAATGATGGGATATAACGAGTCCCACCTGTAGTCAGGTTAGAGGA
1 ACCTGTAAG-CAGGTTAGAGGAATGATGGGATATAACGAGTCCCACCTGTAGTCAGGTTAGAGGA
1151984 ATGATGGGATATAACGAGTCCCACCT
65 ATGATGGGATATAACGAGTCCCACCT
* * *** **
1152010 AGCTGTAAGCAGGTTAGAGGAATTATGGGATACCGCGAGTCATACCTGTAGTCAGGTTAGAGGAA
1 ACCTGTAAGCAGGTTAGAGGAATGATGGGATATAACGAGTCCCACCTGTAGTCAGGTTAGAGGAA
*
1152075 TGATGGGATATAACGAGTCCTACCT
66 TGATGGGATATAACGAGTCCCACCT
1152100 GTAGGCAAGT
Statistics
Matches: 159, Mismatches: 14, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
85 3 0.02
86 72 0.45
88 2 0.01
90 80 0.50
91 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.24
Consensus pattern (90 bp):
ACCTGTAAGCAGGTTAGAGGAATGATGGGATATAACGAGTCCCACCTGTAGTCAGGTTAGAGGAA
TGATGGGATATAACGAGTCCCACCT
Found at i:1152066 original size:133 final size:129
Alignment explanation
Indices: 1151832--1152111 Score: 488
Period size: 133 Copynumber: 2.1 Consensus size: 129
1151822 CATCCCTTTA
*
1151832 CCACCTGTAGGCAGTTTAGAGGAATGATGGGATATAACGAGTCCCACCTGTAAGCAGGTTAGAGG
1 CCACCTGTAGGCAGGTTAGAGGAATGATGGGATATAACGAGTCCCACCTGTAAGCAGGTTAGAGG
1151897 AATTATGGGATACCGCGAGTCATACCTGTAGTCAGGTTAGAGGAATGATGGGATATAACGAGTC
66 AATTATGGGATACCGCGAGTCATACCTGTAGTCAGGTTAGAGGAATGATGGGATATAACGAGTC
*
1151961 CCACCTGTAGTCAGGTTAGAGGAATGATGGGATATAACGAGTCCCACCTAGCTGTAAGCAGGTTA
1 CCACCTGTAGGCAGGTTAGAGGAATGATGGGATATAACGAGTCCCA-C---CTGTAAGCAGGTTA
1152026 GAGGAATTATGGGATACCGCGAGTCATACCTGTAGTCAGGTTAGAGGAATGATGGGATATAACGA
62 GAGGAATTATGGGATACCGCGAGTCATACCTGTAGTCAGGTTAGAGGAATGATGGGATATAACGA
1152091 GTC
127 GTC
* *
1152094 CTACCTGTAGGCAAGTTA
1 CCACCTGTAGGCAGGTTA
1152112 AAGCAACATT
Statistics
Matches: 142, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
129 44 0.31
130 1 0.01
133 97 0.68
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.24
Consensus pattern (129 bp):
CCACCTGTAGGCAGGTTAGAGGAATGATGGGATATAACGAGTCCCACCTGTAAGCAGGTTAGAGG
AATTATGGGATACCGCGAGTCATACCTGTAGTCAGGTTAGAGGAATGATGGGATATAACGAGTC
Found at i:1152586 original size:43 final size:43
Alignment explanation
Indices: 1152378--1153106 Score: 494
Period size: 43 Copynumber: 17.0 Consensus size: 43
1152368 CATCTGAAGA
* * * * *
1152378 CAGGTTTGACGGATGATGGGATAT-A-GAGTCCAACCTGTAGG
1 CAGGTTAGAGGGATGATGGGATATAATAAATCCCACCTGTAGG
* * * *** * *
1152419 CTGGTTAGAGGAATGATGGGATCTAATGGGT-CAACCCTGTTGG
1 CAGGTTAGAGGGATGATGGGATATAATAAATCCCA-CCTGTAGG
* * * ** * ** *
1152462 CAGGTTGGAGGGATAATGGAATATAACGAGTCATACTTGTAGG
1 CAGGTTAGAGGGATGATGGGATATAATAAATCCCACCTGTAGG
* * * * * ** **
1152505 CGGGTCAGAGGAATGATGGGATTTGATGTATCATACCTG-AGGG
1 CAGGTTAGAGGGATGATGGGATATAATAAATCCCACCTGTA-GG
*
1152548 CAGGTTGGAGGGATGATGGGATATAATAAATCCCACCTGTAGG
1 CAGGTTAGAGGGATGATGGGATATAATAAATCCCACCTGTAGG
* * * * **
1152591 CAGGTTTGAGGGAAGATGGGATATGGAGTCTAA-CCGTCCTGTAGG
1 CAGGTTAGAGGGATGATGGGATAT--AAT-AAATCCCACCTGTAGG
* * * * * *
1152636 TAGGTTAAAGAGATGATGAGATATAATGAGTCCCACCTGT-GAG
1 CAGGTTAGAGGGATGATGGGATATAATAAATCCCACCTGTAG-G
* * * **
1152679 CAGGTTAGAGTGATGATTGGATATAATAAATCCCACTTGTAAC
1 CAGGTTAGAGGGATGATGGGATATAATAAATCCCACCTGTAGG
* * * *
1152722 CAGGTTAGAGGGGTGATTGGATATAATAAATCCCACTTGTAAG
1 CAGGTTAGAGGGATGATGGGATATAATAAATCCCACCTGTAGG
* * * **
1152765 CAGGTTAAAGGGATGATGGGATATAATAAATCCCGCTTGTAAC
1 CAGGTTAGAGGGATGATGGGATATAATAAATCCCACCTGTAGG
* * *
1152808 CAAGTTAGAGGGGTGATGGGATATAATAAATCCCAACTGTAGG
1 CAGGTTAGAGGGATGATGGGATATAATAAATCCCACCTGTAGG
* *
1152851 CAGGTT-GAAGGAATGATGGGATATAATAAATTCCACCTGTAGG
1 CAGGTTAG-AGGGATGATGGGATATAATAAATCCCACCTGTAGG
* * *
1152894 CAGGTTAGAGGAATGATGGGAT-TAACAAGTCCCACCTG-AGGG
1 CAGGTTAGAGGGATGATGGGATATAATAAATCCCACCTGTA-GG
* * * *
1152936 CAGGTTTGAGGGATGATGGGATATAGT--GTCCAACCTGTAGG
1 CAGGTTAGAGGGATGATGGGATATAATAAATCCCACCTGTAGG
** * * *
1152977 CAGGTTAGAGGGATGATGGGATATAACGAGTCCCTCCTGTAGA
1 CAGGTTAGAGGGATGATGGGATATAATAAATCCCACCTGTAGG
* * * * * * * **
1153020 C-GTATTAGAAAGAAT-ATGGGATATAATGAGTCCTATCTGTAAA
1 CAG-GTTAG-AGGGATGATGGGATATAATAAATCCCACCTGTAGG
* * *
1153063 CAGGTTAGAGGGATGATGGGATATCATGAATCCAACCTGTAGG
1 CAGGTTAGAGGGATGATGGGATATAATAAATCCCACCTGTAGG
1153106 C
1 C
1153107 GTTCGTCCTG
Statistics
Matches: 545, Mismatches: 120, Indels: 44
0.77 0.17 0.06
Matches are distributed among these distances:
41 55 0.10
42 49 0.09
43 401 0.74
44 8 0.01
45 30 0.06
46 2 0.00
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.25
Consensus pattern (43 bp):
CAGGTTAGAGGGATGATGGGATATAATAAATCCCACCTGTAGG
Found at i:1160258 original size:2 final size:2
Alignment explanation
Indices: 1160202--1160240 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1160192 CGATTAAAAT
1160202 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1160241 GTATTTGTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1160492 original size:2 final size:2
Alignment explanation
Indices: 1160485--1160553 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
1160475 NNNNNNNNNN
1160485 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1160527 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1160554 AATACCTCAA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Done.