Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold330
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1763736
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 499 characters in sequence are not A, C, G, or T
File 10 of 14
Found at i:1190365 original size:61 final size:56
Alignment explanation
Indices: 1190047--1190355 Score: 303
Period size: 61 Copynumber: 5.4 Consensus size: 56
1190037 TCCTTTCACC
*
1190047 CTTTAGTCCTCAAAGAGCAAGACGCCT--TTT-AAAGCCCACACAAGTTGGTGGCA
1 CTTTAGTCCTCAAAGAGCAGGACGCCTCCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
1190100 CCTTTAGTCCTCAAAGAGCAGGATG---CCTTTCAAAGCCCACACGAGTTGGTGGCA
1 -CTTTAGTCCTCAAAGAGCAGGACGCCTCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * * *
1190154 CTTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTCAAAGTCCACACAAGTTGGTGGCGC
1 CTTTAGTCCTCAAAGAGCAGGACGCC---TCCTTTCAAAGCCCACACAAGTTGGTGGC-A
* *
1190214 CTTTTAGTCCTCAAAGAGCAAGACG---CCTTTCAAAGCCCACACAAGCTGGTGGCA
1 C-TTTAGTCCTCAAAGAGCAGGACGCCTCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
1190268 CCTTTTAGTCCTCAAAGAGTAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 -C-TTTAGTCCTCAAAGAGCAGGACGCC---TCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
1190329 CTTCCCAGTCCTCAAAAAGTAGGACGC
1 CTT--TAGTCCTCAAAGAGCAGGACGC
1190356 TCCCTCCTTT
Statistics
Matches: 214, Mismatches: 21, Indels: 33
0.80 0.08 0.12
Matches are distributed among these distances:
53 26 0.12
54 44 0.21
55 48 0.22
59 28 0.13
60 2 0.01
61 66 0.31
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (56 bp):
CTTTAGTCCTCAAAGAGCAGGACGCCTCCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:1190494 original size:155 final size:155
Alignment explanation
Indices: 1190211--1190510 Score: 512
Period size: 155 Copynumber: 1.9 Consensus size: 155
1190201 AAGTTGGTGG
1190211 CGCCTTTTAGTCCTCAAAGAGCAAGACGCCTTTCAAAGCCCACACAAGCTGGTGGCACCTTTTAG
1 CGCCTTTTAGTCCTCAAAGAGCAAGACGCCTTTCAAAGCCCACACAAGCTGGTGGCACCTTTTAG
* * *
1190276 TCCTCAAAGAGTAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCT
66 TCCTCAAAGAGCAAGATGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCT
1190341 CAAAAAGTAGGACGCTCCCTCCTTT
131 CAAAAAGTAGGACGCTCCCTCCTTT
* * *
1190366 CGCCTTTTTGTCCTCAAAGAGCAGGATGCCATTT-AAAGCCCACACAAGCTGGTGGCACCTTTTA
1 CGCCTTTTAGTCCTCAAAGAGCAAGACGCC-TTTCAAAGCCCACACAAGCTGGTGGCACCTTTTA
*
1190430 GTCCTCAAAGAGCAAGATGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCC
65 GTCCTCAAAGAGCAAGATGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCC
*
1190495 TCAAAGAGTAGGACGC
130 TCAAAAAGTAGGACGC
1190511 CTTTCAAAGC
Statistics
Matches: 136, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
155 133 0.98
156 3 0.02
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (155 bp):
CGCCTTTTAGTCCTCAAAGAGCAAGACGCCTTTCAAAGCCCACACAAGCTGGTGGCACCTTTTAG
TCCTCAAAGAGCAAGATGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCT
CAAAAAGTAGGACGCTCCCTCCTTT
Found at i:1190495 original size:271 final size:263
Alignment explanation
Indices: 1190100--1190770 Score: 875
Period size: 265 Copynumber: 2.5 Consensus size: 263
1190090 GTTGGTGGCA
*
1190100 CCTTTAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACGAGTTGGTGGCA-CTTCAGTCCT
1 CCTTTAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACGAGTTGGTGGCACCTTTAGTCCT
* * * *
1190164 CAAAGAGCAGGATGCCTTTTCCTTTCAAAGTCCACACAAGTTGGTGGCGCCTTTTAGTCCTCAAA
66 CAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGC-ACTTCTAGTCCTCAAA
* *
1190229 GAGCAAGACGCCTTTCAAAGCCCACACAAGCTGGTGGCACCTTTTAGTCCTCAAAGAGTAGGATG
130 GAGCAAGACGCCTTTCAAAGCCCACACAAGCTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGA--
* *
1190294 CCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCCAGTCCTCAAAAAG-TAGGACGCT
193 -C---GCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CCAGTCCTCAAAAAGCAAGG-CGCT
*
1190357 CCCTCCTT-TCGC
252 CCCT-CTTGTCAC
* * * *
1190369 CTTTTTGTCCTCAAAGAGCAGGATGCCATTT-AAAGCCCACACAAGCTGGTGGCACCTTTTAGTC
1 CCTTTAGTCCTCAAAGAGCAGGATGCC-TTTCAAAGCCCACACGAGTTGGTGGCACC-TTTAGTC
* *
1190433 CTCAAAGAGCAAGATGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCA
64 CTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTT-CTAGTCCTCA
* * ** *
1190498 AAGAGTAGGACGCCTTTCAAAGCCCACATGAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGA
128 AAGAGCAAGACGCCTTTCAAAGCCCACACAAGCTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGA
* * *
1190563 CGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAAGGCGCTCTCTCT
193 CGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAAAGCAAGGCGCTCCCTCT
1190628 TGTCAC
258 TGTCAC
* *** *
1190634 CCTTTAGTCCTCAGAGAGCAGGACATCTTTCAAAGCCCACACGAGTTGGTGGCACCCTCTAGTCC
1 CCTTTAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACGAGTTGGTGGCA-CCTTTAGTCC
* * *
1190699 TCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTGTAGTCCTCA
65 TCAAAGAGCAGGATGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCAC-TTCTAGTCCTCA
1190764 AAGAGCA
128 AAGAGCA
1190771 GGACTCACTT
Statistics
Matches: 352, Mismatches: 39, Indels: 25
0.85 0.09 0.06
Matches are distributed among these distances:
264 6 0.02
265 124 0.35
266 47 0.13
267 2 0.01
268 1 0.00
269 46 0.13
270 7 0.02
271 119 0.34
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (263 bp):
CCTTTAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACGAGTTGGTGGCACCTTTAGTCCT
CAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCTAGTCCTCAAAG
AGCAAGACGCCTTTCAAAGCCCACACAAGCTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGC
CTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAAAGCAAGGCGCTCCCTCTTGT
CAC
Found at i:1190539 original size:55 final size:55
Alignment explanation
Indices: 1190375--1190614 Score: 297
Period size: 55 Copynumber: 4.3 Consensus size: 55
1190365 TCGCCTTTTT
* * *
1190375 GTCCTCAAAGAGCAGGATGCCATTT-AAAGCCCACACAAGCTGGTGGCACCTTTTA
1 GTCCTCAAAGAGCAGGACGCC-TTTCAAAGCCCACACAAGTTGGTGGCACCTTCTA
* *
1190430 GTCCTCAAAGAGCAAGATGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCTA
1 GTCCTCAAAGAGCAGGACGCCTT-T-C----AAAGCCCACACAAGTTGGTGGCACCTT-CTA
* **
1190491 GTCCTCAAAGAGTAGGACGCCTTTCAAAGCCCACATGAGTTGGTGGCACCTT-TCA
1 GTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCT-A
*
1190546 GTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTA
1 GTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCTA
1190601 GTCCTCAAAGAGCA
1 GTCCTCAAAGAGCA
1190615 AGGCGCTCTC
Statistics
Matches: 162, Mismatches: 12, Indels: 22
0.83 0.06 0.11
Matches are distributed among these distances:
54 3 0.02
55 106 0.65
56 4 0.02
59 1 0.01
60 4 0.02
61 44 0.27
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (55 bp):
GTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCTA
Found at i:1190697 original size:55 final size:57
Alignment explanation
Indices: 1190631--1190775 Score: 168
Period size: 62 Copynumber: 2.5 Consensus size: 57
1190621 TCTCTCTTGT
* * *
1190631 CACCCTTTAGTCCTCAGAGAGCAGGAC-ATC-TTTCAAAGCCCACACGAGTTGGTGG
1 CACCCTCTAGTCCTCAAAGAGCAGGACTATCTTTTCAAAGCCCACACAAGTTGGTGG
*
1190686 CACCCTCTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGG
1 CACCCTCTAGTCCTCAAAGAGCAGGA---C--TATCTTTTCAAAGCCCACACAAGTTGGTGG
** *
1190748 CACTTTGTAGTCCTCAAAGAGCAGGACT
1 CACCCTCTAGTCCTCAAAGAGCAGGACT
1190776 CACTTTATTT
Statistics
Matches: 76, Mismatches: 7, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
55 24 0.32
57 1 0.01
58 1 0.01
59 1 0.01
61 2 0.03
62 47 0.62
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (57 bp):
CACCCTCTAGTCCTCAAAGAGCAGGACTATCTTTTCAAAGCCCACACAAGTTGGTGG
Found at i:1190813 original size:42 final size:43
Alignment explanation
Indices: 1190757--1190911 Score: 176
Period size: 42 Copynumber: 3.6 Consensus size: 43
1190747 GCACTTTGTA
*
1190757 GTCCTCAAAGAGCAGGACTCACTTTATTTTCCTCTTTCT-TTT
1 GTCCTCAAAGAGCAGGACGCACTTTATTTTCCTCTTTCTCTTT
*
1190799 GTCCTCAAAGAGCAGGACGCA-TTTCGTTTTCCT-TTTCTCCTTT
1 GTCCTCAAAGAGCAGGACGCACTTT-ATTTTCCTCTTTCT-CTTT
* * *
1190842 GTCCTCAAAGAGCAGGACGCTCTTTA-TTTCCTTCTTTTCCCTCCTA
1 GTCCTCAAAGAGCAGGACGCACTTTATTTTCC-TC-TTT--CTCTTT
1190888 GTCCTCAAAGAGCAGGACGC-CTTT
1 GTCCTCAAAGAGCAGGACGCACTTT
1190912 TAAAGCCCAC
Statistics
Matches: 98, Mismatches: 6, Indels: 15
0.82 0.05 0.13
Matches are distributed among these distances:
41 8 0.08
42 32 0.33
43 24 0.24
44 3 0.03
45 7 0.07
46 22 0.22
47 2 0.02
ACGTcount: A:0.19, C:0.29, G:0.15, T:0.37
Consensus pattern (43 bp):
GTCCTCAAAGAGCAGGACGCACTTTATTTTCCTCTTTCTCTTT
Found at i:1191011 original size:94 final size:94
Alignment explanation
Indices: 1190886--1191056 Score: 306
Period size: 94 Copynumber: 1.8 Consensus size: 94
1190876 TTTTCCCTCC
* *
1190886 TAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAA
1 TAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCCTCTAGTCCTCAA
*
1190951 AGAGCAGGACGCTCTCTCTTTTCACCTTT
66 AGAGCAGAACGCTCTCTCTTTTCACCTTT
*
1190980 TAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACCCTCTAGTCCTCAA
1 TAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCCTCTAGTCCTCAA
1191045 AGAGCAGAACGC
66 AGAGCAGAACGC
1191057 CTTTTTCTTT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
94 73 1.00
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.22
Consensus pattern (94 bp):
TAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCCTCTAGTCCTCAA
AGAGCAGAACGCTCTCTCTTTTCACCTTT
Found at i:1191045 original size:55 final size:58
Alignment explanation
Indices: 1190980--1191111 Score: 162
Period size: 62 Copynumber: 2.3 Consensus size: 58
1190970 TTTCACCTTT
* *
1190980 TAGTCCTCAAAGAGCAGGACG-C-C-TTTCAAAGCCCACACGAGTTGGTGGCACCCTC
1 TAGTCCTCAAAGAGCAGAACGCCTCTTTTCAAAGCCCACACAAGTTGGTGGCACCCTC
** *
1191035 TAGTCCTCAAAGAGCAGAACGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTG
1 TAGTCCTCAAAGAGCAGAACGCC----TCTTTTCAAAGCCCACACAAGTTGGTGGCACCCTC
1191097 TAGTCCTCAAAGAGC
1 TAGTCCTCAAAGAGC
1191112 GAAACTCACT
Statistics
Matches: 65, Mismatches: 5, Indels: 7
0.84 0.06 0.09
Matches are distributed among these distances:
55 20 0.31
56 1 0.02
61 1 0.02
62 43 0.66
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (58 bp):
TAGTCCTCAAAGAGCAGAACGCCTCTTTTCAAAGCCCACACAAGTTGGTGGCACCCTC
Found at i:1191204 original size:46 final size:46
Alignment explanation
Indices: 1191141--1191335 Score: 212
Period size: 46 Copynumber: 4.4 Consensus size: 46
1191131 TCTTTCTTTT
* *
1191141 GTCCTCAAAGAGTAGGACGCTCTTTATTTCCTTCTTTTCCCTTCTA
1 GTCCTCAAAGAGCAGGACACTCTTTATTTCCTTCTTTTCCCTTCTA
* *
1191187 GTCCTCAAAAAGCAGGACACAT-TTCGT-TTTCCTT-TTCT-CCTT-T-
1 GTCCTCAAAGAGCAGGACAC-TCTT--TATTTCCTTCTTTTCCCTTCTA
1191230 GTCCTCAAAGAGCAGGACACTCTTTATTTCCTTCTTTTCCCTTCTA
1 GTCCTCAAAGAGCAGGACACTCTTTATTTCCTTCTTTTCCCTTCTA
* * * *
1191276 GTCCCCAAAGAGCAGGACACACTTTATTT--TCCTTTT-CCTT-TT
1 GTCCTCAAAGAGCAGGACACTCTTTATTTCCTTCTTTTCCCTTCTA
*
1191318 GTCCTCAGAGAGCAGGAC
1 GTCCTCAAAGAGCAGGAC
1191336 GTATTTCGTT
Statistics
Matches: 128, Mismatches: 12, Indels: 22
0.79 0.07 0.14
Matches are distributed among these distances:
41 1 0.01
42 25 0.20
43 28 0.22
44 11 0.09
45 5 0.04
46 49 0.38
47 8 0.06
48 1 0.01
ACGTcount: A:0.21, C:0.29, G:0.14, T:0.37
Consensus pattern (46 bp):
GTCCTCAAAGAGCAGGACACTCTTTATTTCCTTCTTTTCCCTTCTA
Found at i:1191236 original size:342 final size:340
Alignment explanation
Indices: 1190545--1191247 Score: 1109
Period size: 342 Copynumber: 2.1 Consensus size: 340
1190535 GGCACCTTTC
1190545 AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAA
1 AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAA
* *
1190610 GAGCAAGGCGCTCTCTCTTGTCACCCTTTAGTCCTCAGAGAGCAGGACATCTTTCAAAGCCCACA
66 GAGCAAGGCGCTCTCTCTTGTCACCCTTTAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACA
*
1190675 CGAGTTGGTGGCACCCTCTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACAA
131 CGAGTTGGTGGCACCCTCTAGTCCTCAAAGAGCAGAACGCCTTTTTCTTTTCAAAGCCCACACAA
*
1190740 GTTGGTGGCACTTTGTAGTCCTCAAAGAGCAGGACTCACTTTATTTTCCTCTTTCTTTTGTCCTC
196 GTTGGTGGCACTTTGTAGTCCTCAAAGAGCAGAACTCACTTTATTTTCCTCTTTCTTTTGTCCTC
* *
1190805 AAAGAGCAGGACGCATTTCGTTTTCCTTTTCTCCTTTGTCCTCAAAGAGCAGGACGCTCTTTATT
261 AAAGAGCAGGACGCATTTC-TTTTCCTTTTCTCCTTTGTCCTCAAAAAGCAGGACACTCTTTATT
*
1190870 TCCTTCTTTTCCCTCCT
325 TCCTTCTTCTCCCT-CT
1190887 AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAA
1 AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAA
* * *
1190952 GAGC-AGGACGCTCTCTCTTTTCACCTTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCAC
66 GAGCAAGG-CGCTCTCTCTTGTCACCCTTTAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCAC
1191016 ACGAGTTGGTGGCACCCTCTAGTCCTCAAAGAGCAGAACGCCTTTTTCTTTTCAAAGCCCACACA
130 ACGAGTTGGTGGCACCCTCTAGTCCTCAAAGAGCAGAACGCCTTTTTCTTTTCAAAGCCCACACA
1191081 AGTTGGTGGCACTTTGTAGTCCTCAAAGAGC-GAAACTCACTTTATTTTCCTCTTTCTTTTGTCC
195 AGTTGGTGGCACTTTGTAGTCCTCAAAGAGCAG-AACTCACTTTATTTTCCTCTTTCTTTTGTCC
* *
1191145 TCAAAGAGTAGGACGC-TCTT-TATTTCCTTCTTTTCCCTTCTAGTCCTCAAAAAGCAGGACACA
259 TCAAAGAGCAGGACGCAT-TTCT-TTTCCTT-TTCT-CCTT-T-GTCCTCAAAAAGCAGGACAC-
1191208 T-TTCGT-TTTCCTT-TTCT-CCT-T
317 TCTT--TATTTCCTTCTTCTCCCTCT
*
1191229 TGTCCTCAAAGAGCAGGAC
1 AGTCCTCAAAGAGCAGGAC
1191248 ACTCTTTATT
Statistics
Matches: 337, Mismatches: 13, Indels: 22
0.91 0.03 0.06
Matches are distributed among these distances:
340 1 0.00
341 12 0.04
342 284 0.84
343 4 0.01
344 4 0.01
345 23 0.07
346 8 0.02
347 1 0.00
ACGTcount: A:0.23, C:0.29, G:0.18, T:0.30
Consensus pattern (340 bp):
AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAA
GAGCAAGGCGCTCTCTCTTGTCACCCTTTAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACA
CGAGTTGGTGGCACCCTCTAGTCCTCAAAGAGCAGAACGCCTTTTTCTTTTCAAAGCCCACACAA
GTTGGTGGCACTTTGTAGTCCTCAAAGAGCAGAACTCACTTTATTTTCCTCTTTCTTTTGTCCTC
AAAGAGCAGGACGCATTTCTTTTCCTTTTCTCCTTTGTCCTCAAAAAGCAGGACACTCTTTATTT
CCTTCTTCTCCCTCT
Found at i:1191244 original size:43 final size:42
Alignment explanation
Indices: 1191099--1191368 Score: 171
Period size: 42 Copynumber: 6.2 Consensus size: 42
1191089 GCACTTTGTA
* * *
1191099 GTCCTCAAAGAGC-GAAACTCACTTTATTTTCCTCTTTCT--TTT
1 GTCCTCAAAGAGCAG-GACACA-TTTGTTTTCCT-TTTCTCCTTT
* * *
1191141 GTCCTCAAAGAGTAGGACGC-TCTT-TATTTCCTTCTTTTCCCTTCT
1 GTCCTCAAAGAGCAGGACACAT-TTGT-TTTCCTT-TTCT-CCTT-T
*
1191186 AGTCCTCAAAAAGCAGGACACATTTCGTTTTCCTTTTCTCCTTT
1 -GTCCTCAAAGAGCAGGACACATTT-GTTTTCCTTTTCTCCTTT
*
1191230 GTCCTCAAAGAGCAGGACAC-TCTT-TATTTCCTTCTTTTCCCTTCT
1 GTCCTCAAAGAGCAGGACACAT-TTGT-TTTCCTT-TTCT-CCTT-T
* * *
1191275 AGTCCCCAAAGAGCAGGACACACTTTATTTTCCTTTTC-CTTTT
1 -GTCCTCAAAGAGCAGGACACA-TTTGTTTTCCTTTTCTCCTTT
* ** *
1191318 GTCCTCAGAGAGCAGGACGTATTTCGTTTCCCTTTT-TCCTTT
1 GTCCTCAAAGAGCAGGACACATTT-GTTTTCCTTTTCTCCTTT
*
1191360 GTCTTCAAA
1 GTCCTCAAA
1191369 AAGTGGGACA
Statistics
Matches: 183, Mismatches: 22, Indels: 46
0.73 0.09 0.18
Matches are distributed among these distances:
40 3 0.02
41 15 0.08
42 60 0.33
43 26 0.14
44 10 0.05
45 6 0.03
46 43 0.23
47 17 0.09
48 3 0.02
ACGTcount: A:0.20, C:0.28, G:0.13, T:0.40
Consensus pattern (42 bp):
GTCCTCAAAGAGCAGGACACATTTGTTTTCCTTTTCTCCTTT
Found at i:1191247 original size:89 final size:88
Alignment explanation
Indices: 1191118--1191336 Score: 327
Period size: 89 Copynumber: 2.5 Consensus size: 88
1191108 GAGCGAAACT
*
1191118 CACTTTATTTTCCTCTTTCT-TTTGTCCTCAAAGAGTAGGACGCTCTTTATTTCCTTCTTTTCCC
1 CACTTTATTTTCCT-TTTCTCTTTGTCCTCAAAGAGCAGGACGCTCTTTATTTCCTTCTTTTCCC
*
1191182 TTCTAGTCCTCAAAAAGCAGGACA
65 TTCTAGTCCCCAAAAAGCAGGACA
* *
1191206 CA-TTTCGTTTTCCTTTTCTCCTTTGTCCTCAAAGAGCAGGACACTCTTTATTTCCTTCTTTTCC
1 CACTTT-ATTTTCCTTTTCT-CTTTGTCCTCAAAGAGCAGGACGCTCTTTATTTCCTTCTTTTCC
*
1191270 CTTCTAGTCCCCAAAGAGCAGGACA
64 CTTCTAGTCCCCAAAAAGCAGGACA
*
1191295 CACTTTATTTTCCTTTTC-CTTTTGTCCTCAGAGAGCAGGACG
1 CACTTTATTTTCCTTTTCTC-TTTGTCCTCAAAGAGCAGGACG
1191337 TATTTCGTTT
Statistics
Matches: 118, Mismatches: 8, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
87 9 0.08
88 29 0.25
89 77 0.65
90 3 0.03
ACGTcount: A:0.19, C:0.28, G:0.13, T:0.40
Consensus pattern (88 bp):
CACTTTATTTTCCTTTTCTCTTTGTCCTCAAAGAGCAGGACGCTCTTTATTTCCTTCTTTTCCCT
TCTAGTCCCCAAAAAGCAGGACA
Found at i:1191948 original size:21 final size:21
Alignment explanation
Indices: 1191918--1192015 Score: 160
Period size: 21 Copynumber: 4.7 Consensus size: 21
1191908 TTTTTATCCA
* *
1191918 AATGTCTCGATACATTTGTAT
1 AATGTATCGATACATTTGTAG
*
1191939 AATGTATCGATACATTTATAG
1 AATGTATCGATACATTTGTAG
*
1191960 AATGTATCAATACATTTGTAG
1 AATGTATCGATACATTTGTAG
1191981 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
1192002 AATGTATCGATACA
1 AATGTATCGATACA
1192016 AGGTCCCAAC
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 71 1.00
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:1192098 original size:19 final size:18
Alignment explanation
Indices: 1192074--1192136 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
1192064 ATTCAGTAAA
1192074 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
1192093 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
1192106 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
1192125 TGTATCGATACA
1 TGTATCGATACA
1192137 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:1192111 original size:13 final size:13
Alignment explanation
Indices: 1192093--1192117 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1192083 ACATAAGTGT
1192093 TGTATCGATACAA
1 TGTATCGATACAA
1192106 TGTATCGATACA
1 TGTATCGATACA
1192118 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1192113 original size:32 final size:32
Alignment explanation
Indices: 1192072--1192144 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
1192062 ACATTCAGTA
1192072 AATGTATCGATACATAAGTGTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
*
1192104 AATGTATCGATACATAAGTTTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
1192136 AATGTATCG
1 AATGTATCG
1192145 CTACGAAGCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (32 bp):
AATGTATCGATACATAAGTGTTGTATCGATAC
Found at i:1192187 original size:21 final size:21
Alignment explanation
Indices: 1192161--1192202 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1192151 AGCTACTGCC
1192161 AAGGAAATATATCGATACATT
1 AAGGAAATATATCGATACATT
*
1192182 AAGGAAATGTATCGATACATT
1 AAGGAAATATATCGATACATT
1192203 GTATCGATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.10, G:0.17, T:0.29
Consensus pattern (21 bp):
AAGGAAATATATCGATACATT
Found at i:1192207 original size:13 final size:13
Alignment explanation
Indices: 1192189--1192214 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1192179 ATTAAGGAAA
1192189 TGTATCGATACAT
1 TGTATCGATACAT
1192202 TGTATCGATACAT
1 TGTATCGATACAT
1192215 CAATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1194636 original size:51 final size:53
Alignment explanation
Indices: 1194580--1194698 Score: 172
Period size: 53 Copynumber: 2.3 Consensus size: 53
1194570 TTCTCCGTAA
* * * *
1194580 CGGGGATATTCCAACTCCGATTTTATTT-TC-AAAACACTAA-TTTTCTATAAT
1 CGGGGATACTCCAACTCCGATTTTATTTCCCAAAAACACCAATTTTTC-ACAAT
1194631 CGGGGATACTCCAACTCCGATTTTATTTCCCAAAAACACCAATTTTTCACAAT
1 CGGGGATACTCCAACTCCGATTTTATTTCCCAAAAACACCAATTTTTCACAAT
1194684 CGGGGATACTCCAAC
1 CGGGGATACTCCAAC
1194699 CCCGTTAATC
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
51 27 0.44
52 1 0.02
53 28 0.46
54 5 0.08
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32
Consensus pattern (53 bp):
CGGGGATACTCCAACTCCGATTTTATTTCCCAAAAACACCAATTTTTCACAAT
Found at i:1194712 original size:27 final size:28
Alignment explanation
Indices: 1194682--1194756 Score: 107
Period size: 27 Copynumber: 2.7 Consensus size: 28
1194672 ATTTTTCACA
1194682 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
1194709 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATATC
***
1194737 CGAGGGGATACTCCAACCCC
1 ATCGGGGATACTCCAACCCC
1194757 TACTTTATTC
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 24 0.56
28 19 0.44
ACGTcount: A:0.24, C:0.35, G:0.20, T:0.21
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:1194897 original size:51 final size:51
Alignment explanation
Indices: 1194825--1194978 Score: 170
Period size: 51 Copynumber: 3.0 Consensus size: 51
1194815 CCGAAAGAAG
* * *
1194825 ACTCCAA-TCCCGGTTTCATTTCCAAAACATCAATTTCTCT-TAATCGGGGAT
1 ACTCCAACT-CCGATTTTATTTCCAAAACACCAATTT-TCTATAATCGGGGAT
* * *
1194876 ACTCCAACTCTGATTTTATTTCTAAAACACCCATTTTCTATAATCGGGGAT
1 ACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCTATAATCGGGGAT
* * * *
1194927 ACTCCAACTCCGATTTTATTTCCAAAGCTCCGACTTTTC-ACAATCGGGGAT
1 ACTCCAACTCCGATTTTATTTCCAAAACACC-AATTTTCTATAATCGGGGAT
1194978 A
1 A
1194979 TTCTAACCTC
Statistics
Matches: 87, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
50 3 0.03
51 78 0.90
52 6 0.07
ACGTcount: A:0.28, C:0.27, G:0.12, T:0.34
Consensus pattern (51 bp):
ACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCTATAATCGGGGAT
Found at i:1195073 original size:27 final size:29
Alignment explanation
Indices: 1195043--1195120 Score: 101
Period size: 27 Copynumber: 2.8 Consensus size: 29
1195033 CATCAATTTC
1195043 TCAT-TGGGGATACTCCAACCCCGTTA-A
1 TCATCTGGGGATACTCCAACCCCGTTACA
*
1195070 TCATCT-GGGATACTCCAACCCCGTTACC
1 TCATCTGGGGATACTCCAACCCCGTTACA
**
1195098 TC-TGAGGGGATACTCCAACCCCG
1 TCATCTGGGGATACTCCAACCCCG
1195121 GCTTTATTTC
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
27 25 0.56
28 20 0.44
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.23
Consensus pattern (29 bp):
TCATCTGGGGATACTCCAACCCCGTTACA
Found at i:1195280 original size:52 final size:50
Alignment explanation
Indices: 1195103--1195323 Score: 221
Period size: 51 Copynumber: 4.3 Consensus size: 50
1195093 TTACCTCTGA
* * * ***
1195103 GGGGATACTCCAACCCCGGCTTTATTTCCAAAATATTGA-TTTCTCATAATC
1 GGGGATACTCCAA-CCCGGTTTTATTTTCAAAACACCAATTTTC-CATAATC
* * *
1195154 AGGGATACTCCAACCCTGGTTTTA-TTTCTAAAACACTAATTTTCCACAATC
1 GGGGATACTCCAACCC-GGTTTTATTTTC-AAAACACCAATTTTCCATAATC
*
1195205 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAA-CCCGGTTTTATTTTCAAAACACCAATTTTCC-ATAATC
* * *
1195257 GGGGATACTCCAACTCCGATTTTATTTCTAAAAACACCAATTTTTCATAATC
1 GGGGATACTCCAAC-CCGGTTTTATTT-TCAAAACACCAATTTTCCATAATC
* *
1195309 GAGGATACCCCAACC
1 GGGGATACTCCAACC
1195324 TCATTATTTC
Statistics
Matches: 145, Mismatches: 17, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
50 6 0.04
51 67 0.46
52 56 0.39
53 16 0.11
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (50 bp):
GGGGATACTCCAACCCGGTTTTATTTTCAAAACACCAATTTTCCATAATC
Found at i:1195288 original size:103 final size:103
Alignment explanation
Indices: 1195103--1195323 Score: 268
Period size: 102 Copynumber: 2.1 Consensus size: 103
1195093 TTACCTCTGA
* ***
1195103 GGGGATACTCCAACCCCGGCTTTATTTCCAAAATATTGATTTCTCATAATCAGGGATACTCCAAC
1 GGGGATACTCCAACCCCGGCTTTATTTCCAAAACACCAATTTCTCATAATCAGGGATACTCCAAC
* *
1195168 CCTGGTTTTATTTCT-AAAACACTAATTTTCCACAATC
66 CCTGATTTTATTTCTAAAAACACCAATTTTCCACAATC
* * * *
1195205 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTT-TCCTTTAATCGGGGATACTCCA
1 GGGGATACTCCAACCCCGGCTTTATTTCCAAAACACCAATTTCT-C-ATAATCAGGGATACTCCA
* *
1195269 ACTCC-GATTTTATTTCTAAAAACACCAATTTTTCATAATC
64 AC-CCTGATTTTATTTCTAAAAACACCAATTTTCCACAATC
* *
1195309 GAGGATACCCCAACC
1 GGGGATACTCCAACC
1195324 TCATTATTTC
Statistics
Matches: 101, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
101 1 0.01
102 37 0.37
103 29 0.29
104 34 0.34
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (103 bp):
GGGGATACTCCAACCCCGGCTTTATTTCCAAAACACCAATTTCTCATAATCAGGGATACTCCAAC
CCTGATTTTATTTCTAAAAACACCAATTTTCCACAATC
Found at i:1196403 original size:20 final size:20
Alignment explanation
Indices: 1196358--1196413 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 20
1196348 AGTATCGATA
*
1196358 AATTGTATCGATACATGCTC
1 AATTGTATCGATACATGCAC
*
1196378 -ATTGTATCGATACATGGAC
1 AATTGTATCGATACATGCAC
1196397 AATTGTATCGATACATG
1 AATTGTATCGATACATG
1196414 AGATTGGCAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (20 bp):
AATTGTATCGATACATGCAC
Found at i:1196481 original size:13 final size:13
Alignment explanation
Indices: 1196463--1196511 Score: 63
Period size: 13 Copynumber: 4.2 Consensus size: 13
1196453 CATGGGACAA
1196463 TGTATCGATACAT
1 TGTATCGATACAT
1196476 TGTATCGATACA-
1 TGTATCGATACAT
1196488 TG-AT-GA-A-AT
1 TGTATCGATACAT
1196497 TGTATCGATACAT
1 TGTATCGATACAT
1196510 TG
1 TG
1196512 CTTGTAACAG
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
8 1 0.03
9 3 0.10
10 4 0.13
11 4 0.13
12 3 0.10
13 16 0.52
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1196484 original size:33 final size:34
Alignment explanation
Indices: 1196442--1196511 Score: 108
Period size: 33 Copynumber: 2.1 Consensus size: 34
1196432 CTACCACTGT
1196442 TTGTATCGATACATG-GGACAA-TGTATCGATACA
1 TTGTATCGATACATGAGGA-AATTGTATCGATACA
*
1196475 TTGTATCGATACATGATGAAATTGTATCGATACA
1 TTGTATCGATACATGAGGAAATTGTATCGATACA
1196509 TTG
1 TTG
1196512 CTTGTAACAG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 17 0.50
34 17 0.50
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (34 bp):
TTGTATCGATACATGAGGAAATTGTATCGATACA
Found at i:1204093 original size:11 final size:11
Alignment explanation
Indices: 1204069--1204099 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
1204059 TCTTTCGTAC
1204069 AAAAAAAACAA
1 AAAAAAAACAA
1204080 AAAAATAAACAA
1 AAAAA-AAACAA
1204092 AAAAAAAA
1 AAAAAAAA
1204100 GAAAGGTCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.90, C:0.06, G:0.00, T:0.03
Consensus pattern (11 bp):
AAAAAAAACAA
Found at i:1207272 original size:125 final size:125
Alignment explanation
Indices: 1207049--1207303 Score: 438
Period size: 125 Copynumber: 2.0 Consensus size: 125
1207039 GAAAAAGTGG
1207049 ATGTTTAGGTGATAGTATGGGTAGAGATGGATTGGAGTTGTGTAATGACCAAGAAGGGAATGTTT
1 ATGTTTAGGTGATAGTATGGGTAGAGATGGATTGGAGTTGTGTAATGACCAAGAAGGGAATGTTT
* *
1207114 GGAGGTGTTTTTTTTGGGAGCCGTAAGGAGCTATGGGAATGGACATTTTTATGTGTTTTT
66 GGAGGTGTTTCTTTTGGGAGCCGTAAGGAGCTATGGGAATGGACATTTTTATATGTTTTT
* * * *
1207174 GTGTTTAGGTGATAGTATGGGTAGAGATGGATTGGAGTTGTGTAGTGACCAAGGAGGGAGTGTTT
1 ATGTTTAGGTGATAGTATGGGTAGAGATGGATTGGAGTTGTGTAATGACCAAGAAGGGAATGTTT
* *
1207239 GGAGGTGTTTCTTTTGGGAGCCGTAGGGAGCTATGGGAATGGACTTTTTTATATGTTTTT
66 GGAGGTGTTTCTTTTGGGAGCCGTAAGGAGCTATGGGAATGGACATTTTTATATGTTTTT
1207299 ATGTT
1 ATGTT
1207304 GATGTTTTGC
Statistics
Matches: 121, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
125 121 1.00
ACGTcount: A:0.22, C:0.05, G:0.36, T:0.37
Consensus pattern (125 bp):
ATGTTTAGGTGATAGTATGGGTAGAGATGGATTGGAGTTGTGTAATGACCAAGAAGGGAATGTTT
GGAGGTGTTTCTTTTGGGAGCCGTAAGGAGCTATGGGAATGGACATTTTTATATGTTTTT
Found at i:1208320 original size:44 final size:43
Alignment explanation
Indices: 1208257--1208367 Score: 134
Period size: 44 Copynumber: 2.5 Consensus size: 43
1208247 CCGTGATGTG
* * *
1208257 CCAATGTGCAGATTTAAGGCCTAGACT-TAAAGATAAGAAGGGTA
1 CCAATGTGCTGATTTAAGGCC-AG-CTAAAAAGATAAGAAGAGTA
*
1208301 CCAATGTGCTGATTTAAGGCCAGCTACAAAAGATAAGAAGAGTG
1 CCAATGTGCTGATTTAAGGCCAGCTA-AAAAGATAAGAAGAGTA
* *
1208345 CCAATGTACTGATTCAAGGCCAG
1 CCAATGTGCTGATTTAAGGCCAG
1208368 TGATATTGGA
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
42 2 0.03
43 2 0.03
44 55 0.93
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.22
Consensus pattern (43 bp):
CCAATGTGCTGATTTAAGGCCAGCTAAAAAGATAAGAAGAGTA
Found at i:1208626 original size:28 final size:28
Alignment explanation
Indices: 1208594--1208716 Score: 95
Period size: 28 Copynumber: 4.4 Consensus size: 28
1208584 TGAAAAAAGA
*
1208594 TGCCATTAACCTATGGGCTTTGGAAGGG
1 TGCCATTAACTTATGGGCTTTGGAAGGG
** * ***
1208622 TGCCACCAACTTGTGGGCTTAAAAAGGG
1 TGCCATTAACTTATGGGCTTTGGAAGGG
*
1208650 TGCCACTT-GCTTATGGGCTTTGGAAGGG
1 TGCCA-TTAACTTATGGGCTTTGGAAGGG
* * * ***
1208678 TGCCACTGACTTGTGGGCTTAAAAAGGG
1 TGCCATTAACTTATGGGCTTTGGAAGGG
*
1208706 TGCCACTAACT
1 TGCCATTAACT
1208717 GACCTGTGGG
Statistics
Matches: 72, Mismatches: 21, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
27 1 0.01
28 71 0.99
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (28 bp):
TGCCATTAACTTATGGGCTTTGGAAGGG
Found at i:1208654 original size:56 final size:56
Alignment explanation
Indices: 1208575--1208715 Score: 185
Period size: 56 Copynumber: 2.5 Consensus size: 56
1208565 CACTAATTTG
* *
1208575 TGTGGGCCTTGAAAAAAGATGCCATTAACCTATGGGCTTTGGAAGGGTGCCACCAACT
1 TGTGGG-CTT-AAAAAGGGTGCCATTAACCTATGGGCTTTGGAAGGGTGCCACCAACT
* * **
1208633 TGTGGGCTTAAAAAGGGTGCCACTT-GCTTATGGGCTTTGGAAGGGTGCCACTGACT
1 TGTGGGCTTAAAAAGGGTGCCA-TTAACCTATGGGCTTTGGAAGGGTGCCACCAACT
*
1208689 TGTGGGCTTAAAAAGGGTGCCACTAAC
1 TGTGGGCTTAAAAAGGGTGCCATTAAC
1208716 TGACCTGTGG
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
55 1 0.01
56 61 0.84
57 5 0.07
58 6 0.08
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (56 bp):
TGTGGGCTTAAAAAGGGTGCCATTAACCTATGGGCTTTGGAAGGGTGCCACCAACT
Found at i:1208718 original size:32 final size:31
Alignment explanation
Indices: 1208630--1208729 Score: 104
Period size: 28 Copynumber: 3.4 Consensus size: 31
1208620 GGTGCCACCA
1208630 ACTTGTGGGCTTAAAAAGGGTGCCACT--TG
1 ACTTGTGGGCTTAAAAAGGGTGCCACTACTG
* ***
1208659 -CTTATGGGCTTTGGAAGGGTG-C-C-ACTG
1 ACTTGTGGGCTTAAAAAGGGTGCCACTACTG
1208686 ACTTGTGGGCTTAAAAAGGGTGCCACTAACTG
1 ACTTGTGGGCTTAAAAAGGGTGCCACT-ACTG
*
1208718 ACCTGTGGGCTT
1 ACTTGTGGGCTT
1208730 TGAAAAGATG
Statistics
Matches: 55, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
26 1 0.02
27 3 0.05
28 34 0.62
29 1 0.02
30 1 0.02
32 15 0.27
ACGTcount: A:0.21, C:0.19, G:0.32, T:0.28
Consensus pattern (31 bp):
ACTTGTGGGCTTAAAAAGGGTGCCACTACTG
Found at i:1208761 original size:28 final size:28
Alignment explanation
Indices: 1208714--1208963 Score: 302
Period size: 28 Copynumber: 8.9 Consensus size: 28
1208704 GGTGCCACTA
1208714 ACTGACCTGTGGGCTTTGAAAAGATGCC
1 ACTGACCTGTGGGCTTTGAAAAGATGCC
* * *
1208742 ACTAACATGTGGACTTTGAAAAGATGCC
1 ACTGACCTGTGGGCTTTGAAAAGATGCC
* * *
1208770 ACTAACATGTGGACTTTGAAAAGATGCC
1 ACTGACCTGTGGGCTTTGAAAAGATGCC
*
1208798 ACTGACCTGTGGGCTTTGAAAGGATGCC
1 ACTGACCTGTGGGCTTTGAAAAGATGCC
* * *
1208826 ACTGACCTATAGGCTTTGAAGAGATGCC
1 ACTGACCTGTGGGCTTTGAAAAGATGCC
* * * *
1208854 ACCGACTTGTAGGCTTTGAAAGGATGCC
1 ACTGACCTGTGGGCTTTGAAAAGATGCC
* * * *
1208882 ATTGACCTCTAGGCTTTGAAAAAATGCC
1 ACTGACCTGTGGGCTTTGAAAAGATGCC
*
1208910 ACTGACTTGTGGGCTTTGAAAAGATGCC
1 ACTGACCTGTGGGCTTTGAAAAGATGCC
* * *
1208938 ACTGACTTGTGGGCTTTCAAGAGATG
1 ACTGACCTGTGGGCTTTGAAAAGATG
1208964 AACGTTCTAG
Statistics
Matches: 193, Mismatches: 29, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 193 1.00
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (28 bp):
ACTGACCTGTGGGCTTTGAAAAGATGCC
Found at i:1208799 original size:56 final size:55
Alignment explanation
Indices: 1208678--1208963 Score: 295
Period size: 56 Copynumber: 5.0 Consensus size: 55
1208668 TTTGGAAGGG
* *
1208678 TGCCACTGACTTGTGGGC-TTAAAAAGGGTGCCACTAACTGACCTGTGGGCTTTGAAAAGA
1 TGCCACTGACTTGTGGGCTTTGAAAA-GATG-C-C--ACTGACCTGT-GGCTTTGAAAAGA
* * * * *
1208738 TGCCACTAACATGTGGACTTTGAAAAGATGCCACTAACATGTGGACTTTGAAAAGA
1 TGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACCTGTGG-CTTTGAAAAGA
* * * *
1208794 TGCCACTGACCTGTGGGCTTTGAAAGGATGCCACTGACCTATAGGCTTTGAAGAGA
1 TGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACCTGT-GGCTTTGAAAAGA
* * * * * *
1208850 TGCCACCGACTTGTAGGCTTTGAAAGGATGCCATTGACCTCTAGGCTTTGAAAAAA
1 TGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACCTGT-GGCTTTGAAAAGA
* * *
1208906 TGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTCAAGAGA
1 TGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACCTGT-GGCTTTGAAAAGA
1208962 TG
1 TG
1208964 AACGTTCTAG
Statistics
Matches: 191, Mismatches: 32, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
55 2 0.01
56 161 0.84
57 2 0.01
58 1 0.01
59 1 0.01
60 18 0.09
61 6 0.03
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (55 bp):
TGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACCTGTGGCTTTGAAAAGA
Found at i:1215137 original size:33 final size:33
Alignment explanation
Indices: 1215100--1215166 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1215090 TTCAACGATC
1215100 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1215133 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1215166 T
1 T
1215167 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1215138 original size:13 final size:13
Alignment explanation
Indices: 1215120--1215144 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1215110 CATAAAATGT
1215120 TGTATCGATACAA
1 TGTATCGATACAA
1215133 TGTATCGATACA
1 TGTATCGATACA
1215145 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1215228 original size:13 final size:13
Alignment explanation
Indices: 1215210--1215234 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1215200 ATTACTCACA
1215210 TGTATCGATACAT
1 TGTATCGATACAT
1215223 TGTATCGATACA
1 TGTATCGATACA
1215235 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1215371 original size:52 final size:52
Alignment explanation
Indices: 1215243--1215363 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
1215233 CACTGATCTT
*
1215243 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1215295 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1215347 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
1215364 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1223574 original size:22 final size:21
Alignment explanation
Indices: 1223544--1223589 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 21
1223534 TAGTGACTAT
1223544 ACAAAAAAAATAATAAGAATGA
1 ACAAAAAAAATAA-AAGAATGA
*
1223566 ACAACAAAAATAAAAGAATGA
1 ACAAAAAAAATAAAAGAATGA
1223587 ACA
1 ACA
1223590 TCAATCAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.72, C:0.09, G:0.09, T:0.11
Consensus pattern (21 bp):
ACAAAAAAAATAAAAGAATGA
Found at i:1224620 original size:32 final size:32
Alignment explanation
Indices: 1224584--1224658 Score: 141
Period size: 32 Copynumber: 2.3 Consensus size: 32
1224574 CTGTCTCAAT
1224584 GTGCGCTCGACCCCGATGATAGGGCAAATGAA
1 GTGCGCTCGACCCCGATGATAGGGCAAATGAA
1224616 GTGCGCTCGACCCCGATGATAGGGCAAATGAA
1 GTGCGCTCGACCCCGATGATAGGGCAAATGAA
*
1224648 GTGCGCCCGAC
1 GTGCGCTCGAC
1224659 TTAATACCCC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.25, C:0.28, G:0.32, T:0.15
Consensus pattern (32 bp):
GTGCGCTCGACCCCGATGATAGGGCAAATGAA
Found at i:1227861 original size:20 final size:20
Alignment explanation
Indices: 1227835--1227891 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
1227825 TAAAAGGATA
*
1227835 AAATGTATCGATACATTGA-
1 AAATGTATCGATACATTCAT
1227854 AGAATGTATCGATACATTCAT
1 A-AATGTATCGATACATTCAT
*
1227875 ACATGTATCGATACATT
1 AAATGTATCGATACATT
1227892 TGGGTAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 1 0.03
20 32 0.94
21 1 0.03
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (20 bp):
AAATGTATCGATACATTCAT
Found at i:1229164 original size:28 final size:27
Alignment explanation
Indices: 1229124--1229281 Score: 165
Period size: 28 Copynumber: 5.7 Consensus size: 27
1229114 CTACAATGTT
*
1229124 CATCTTTTCAAAGCCCACAAGTTAGTGG
1 CATC-TTTCAAAGCCCACAAGTCAGTGG
1229152 CATCATTTCAAAGCCCACAAGTCAGTGG
1 CATC-TTTCAAAGCCCACAAGTCAGTGG
1229180 CATCTCTTCAAAG-CCACAAGTCAGTGG
1 CATCT-TTCAAAGCCCACAAGTCAGTGG
* * * *
1229207 CATCCATTCACATCCAACAAGTCAGTGG
1 CAT-CTTTCAAAGCCCACAAGTCAGTGG
* * *
1229235 CATCTCTTCAAAGCCCATAGGTCAGTAG
1 CATCT-TTCAAAGCCCACAAGTCAGTGG
* *
1229263 TATCCTTTCAAAGTCCACA
1 CAT-CTTTCAAAGCCCACA
1229282 GCTCAAGCTT
Statistics
Matches: 109, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
27 24 0.22
28 83 0.76
29 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (27 bp):
CATCTTTCAAAGCCCACAAGTCAGTGG
Found at i:1229209 original size:55 final size:55
Alignment explanation
Indices: 1229124--1229281 Score: 185
Period size: 55 Copynumber: 2.8 Consensus size: 55
1229114 CTACAATGTT
* *
1229124 CATCTTTTCAAAGCCCACAAGTTAGTGGCATCATTTCAAAGCCCACAAGTCAGTGG
1 CATCTCTTCAAAG-CCACAAGTCAGTGGCATCATTTCAAAGCCCACAAGTCAGTGG
* * *
1229180 CATCTCTTCAAAGCCACAAGTCAGTGGCATCCA-TTCACATCCAACAAGTCAGTGG
1 CATCTCTTCAAAGCCACAAGTCAGTGGCAT-CATTTCAAAGCCCACAAGTCAGTGG
* * * *
1229235 CATCTCTTCAAAGCC-CATAGGTCAGTAGTATCCTTTCAAAGTCCACA
1 CATCTCTTCAAAGCCACA-A-GTCAGTGGCATCATTTCAAAGCCCACA
1229282 GCTCAAGCTT
Statistics
Matches: 86, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
54 2 0.02
55 52 0.60
56 32 0.37
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (55 bp):
CATCTCTTCAAAGCCACAAGTCAGTGGCATCATTTCAAAGCCCACAAGTCAGTGG
Found at i:1232088 original size:101 final size:101
Alignment explanation
Indices: 1231811--1232224 Score: 540
Period size: 101 Copynumber: 4.1 Consensus size: 101
1231801 CCCTAGTCGA
* * * * *
1231811 GAATCAACATATTGGCACC-TT-T-ATCTTTAAGTCCAATGTAGTTGGCCTTGAATCAGCACATC
1 GAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATT
1231873 GGCA----C--CTTTAAGTCCAATATCGCTGGCCTT
66 GGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTT
1231903 GAATCAGCATATTGGCGCCTTTGTCATCTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACAT
1 GAATCAGCATATTGGCGCCTTTGTCATC-TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACAT
* *
1231968 TGACACCTTCATCTTTAAGTCCAATATCGCTGTCCTT
65 TGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTT
1232005 GAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATT
1 GAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATT
*
1232070 GGCACCTTCATCTTTAAGTCCAGTATCGCTGGCCTT
66 GGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTT
* ** * *
1232106 GAATCAGCATATTGGCGCCTTCGTCATCTTTAAAACCCAATGTCGTTGGCCTTTAATCAGCACAT
1 GAATCAGCATATTGGCGCCTTTGTCATCTTT-AAGTCCAATGTCGCTGGCCTTGAATCAGCACAT
* * * * *
1232171 TGGCATTCTTCTCATCTTTAAGTCTAATGTCGCTGACCGT
65 TGGCA--CCT-TCATCTTTAAGTCCAATATCGCTGGCCTT
* *
1232211 GAATTAGCACATTG
1 GAATCAGCATATTG
1232225 ACATCCTTTT
Statistics
Matches: 285, Mismatches: 23, Indels: 15
0.88 0.07 0.05
Matches are distributed among these distances:
92 17 0.06
93 2 0.01
94 1 0.00
95 3 0.01
96 37 0.13
100 1 0.00
101 100 0.35
102 86 0.30
104 2 0.01
105 36 0.13
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.33
Consensus pattern (101 bp):
GAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATT
GGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTT
Found at i:1232146 original size:154 final size:153
Alignment explanation
Indices: 1231878--1232224 Score: 414
Period size: 154 Copynumber: 2.3 Consensus size: 153
1231868 ACATCGGCAC
* * *
1231878 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTTAAGTCCAA
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-TTGTCATCTTTTAAGTCCAA
* ** *
1231943 TGTCGCTGGCCTTGAATCAGCACATTGACACCTTCATCTTTAAGTCCAATATCGCTGTCCTTGAA
65 TATCGCTGGCCTTGAATCAGCACATTGACACCTTCATCTTTAAACCCAATATCGCTGGCCTTGAA
* * *
1232008 TCAGCATATTGGCGC-CTTTGTCAT
130 TCAGCACATTGGCACTC-TTCTCAT
*
1232032 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-T-TCATC-TTTAAGTCCAGT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTGTCATCTTTTAAGTCCAAT
* * * * *
1232094 ATCGCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAAACCCAATGTCGTTGGCCTT
66 ATCGCTGGCCTTGAATCAGCACATTGACACC-T--TCATCTTT-AAACCCAATATCGCTGGCCTT
* *
1232159 TAATCAGCACATTGGCATTCTTCTCAT
127 GAATCAGCACATTGGCACTCTTCTCAT
* * * *
1232186 CTTTAAGTCTAATGTCGCTGACCGTGAATTAGCACATTG
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTG
1232225 ACATCCTTTT
Statistics
Matches: 166, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
150 38 0.23
151 6 0.04
152 1 0.01
153 8 0.05
154 112 0.67
155 1 0.01
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.34
Consensus pattern (153 bp):
CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTGTCATCTTTTAAGTCCAAT
ATCGCTGGCCTTGAATCAGCACATTGACACCTTCATCTTTAAACCCAATATCGCTGGCCTTGAAT
CAGCACATTGGCACTCTTCTCAT
Found at i:1232945 original size:13 final size:13
Alignment explanation
Indices: 1232927--1232997 Score: 79
Period size: 13 Copynumber: 5.0 Consensus size: 13
1232917 TTCAACGATT
1232927 TGTATCGATACAA
1 TGTATCGATACAA
1232940 TGTATCGATACATAA
1 TGTATCGATAC--AA
1232955 GTGTCGTATCGATACAA
1 ---T-GTATCGATACAA
1232972 TGTATCGATACAA
1 TGTATCGATACAA
*
1232985 TGTATCGCTACAA
1 TGTATCGATACAA
1232998 AGCTACTGCC
Statistics
Matches: 51, Mismatches: 1, Indels: 12
0.80 0.02 0.19
Matches are distributed among these distances:
13 35 0.69
14 1 0.02
15 2 0.04
17 2 0.04
18 1 0.02
19 10 0.20
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1236968 original size:52 final size:52
Alignment explanation
Indices: 1236898--1237018 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
1236888 GAAAATTTAT
*
1236898 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
1236950 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
1237002 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
1237019 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:1237031 original size:52 final size:51
Alignment explanation
Indices: 1236898--1237038 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
1236888 GAAAATTTAT
1236898 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
1236950 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
1237002 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
1237039 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:1237045 original size:13 final size:13
Alignment explanation
Indices: 1237027--1237051 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1237017 CAAAGATCAG
1237027 TGTATCGATACAA
1 TGTATCGATACAA
1237040 TGTATCGATACA
1 TGTATCGATACA
1237052 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1237135 original size:13 final size:13
Alignment explanation
Indices: 1237117--1237141 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1237107 CAAAAAAATA
1237117 TGTATCGATACAT
1 TGTATCGATACAT
1237130 TGTATCGATACA
1 TGTATCGATACA
1237142 ACATTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1238078 original size:67 final size:68
Alignment explanation
Indices: 1237954--1238080 Score: 175
Period size: 67 Copynumber: 1.9 Consensus size: 68
1237944 ATTGGGTTTT
* * *
1237954 AAAGATGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATG
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATG
1238019 AGA
66 AGA
* * * * *
1238022 AAAG-TGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTGAAGATGA
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGA
1238081 TGAAAAAGGA
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
67 47 0.92
68 4 0.08
ACGTcount: A:0.38, C:0.12, G:0.26, T:0.24
Consensus pattern (68 bp):
AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATG
AGA
Found at i:1238234 original size:49 final size:49
Alignment explanation
Indices: 1238094--1238941 Score: 1019
Period size: 49 Copynumber: 17.7 Consensus size: 49
1238084 AAAAGGATGT
* *
1238094 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* * *
1238146 CGATATGCTGATTCAAGGCCAAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCC-AGCTACATTGGACTTAAAGATGAAGGTGC
* * *
1238196 CAATGTGCTGAGTCAAGGCTAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * * *
1238245 CAATATGCTGATTCAAGGCCAGCTATA-TGGGCTTAATGGTGCAA-GTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG-AAGGTGC
* *
1238293 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
1238342 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
1238391 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGATGATGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
1238440 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
**
1238483 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGACGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * * *
1238532 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGATGATGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
1238581 CAATTTGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
**
1238624 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGACGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
1238673 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1238716 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
1238765 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGATGATGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
1238814 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
1238857 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
1238906 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
1238942 GAAGGGTTGC
Statistics
Matches: 681, Mismatches: 87, Indels: 59
0.82 0.11 0.07
Matches are distributed among these distances:
43 148 0.22
45 4 0.01
47 4 0.01
48 40 0.06
49 425 0.62
50 22 0.03
52 19 0.03
53 19 0.03
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.25
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
Found at i:1238506 original size:92 final size:93
Alignment explanation
Indices: 1238084--1238946 Score: 993
Period size: 92 Copynumber: 9.1 Consensus size: 93
1238074 AAGATGATGA
* * * *
1238084 AAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCGA
1 AAAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-GAAGA--TGCCAA
1238149 TATGCTGATTCAAGGCCAAGCTATATTGGACTT
62 TATGCTGATTCAAGGCC-AGCTATATTGGACTT
* * * *
1238182 AAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCTAGCTACATTGGACTTAAAGATAAAGGTGCCA
1 --A-A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCA
*
1238247 ATATGCTGATTCAAGGCCAGCTATA-TGGGCTT
61 ATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * *
1238279 AATGGTGCAA-GTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCC
1 AA------AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCC
1238343 AATATGCTGATTCAAGGCCAGCTATATTGGACTT
60 AATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
1238377 AATGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGATGATGCCA
1 AA-----AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCA
*
1238442 ATATGCTGATTCAAGGCCAGCGATATTGGACTT
61 ATATGCTGATTCAAGGCCAGCTATATTGGACTT
*
1238475 -AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGACGCCAATATG
1 AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATG
*
1238539 CTGATTCAAGGCCAGCGATATTGGACTT
66 CTGATTCAAGGCCAGCTATATTGGACTT
* * *
1238567 AAAGATGATGATGCCAATTTGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-G--G-TGCCA
1 AAA-A-G--G-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCA
* *
1238626 ATGTGCTGATTCAAGGCCAGCTACATTGGACTT
61 ATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * * *
1238659 AAAGATGAAGACGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-G--G-TGCCA
1 AAA-A-G--G-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCA
* *
1238718 ATGTGCTGATTCAAGGCCAGCTACATTGGACTT
61 ATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
1238751 AAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGATGATGCCA
1 --A-A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCA
*
1238816 ATATGCTGATTCAAGGCCAGCGATATTGGACTT
61 ATATGCTGATTCAAGGCCAGCTATATTGGACTT
1238849 -AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATG
1 AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATG
*
1238913 CTGATTCAAGGCCAGCTATATTGGGCTT
66 CTGATTCAAGGCCAGCTATATTGGACTT
*
1238941 AGAAGG
1 AAAAGG
1238947 GTTGCCACCG
Statistics
Matches: 689, Mismatches: 47, Indels: 61
0.86 0.06 0.08
Matches are distributed among these distances:
92 331 0.48
93 10 0.01
94 5 0.01
95 6 0.01
96 2 0.00
97 94 0.14
98 171 0.25
99 22 0.03
100 1 0.00
101 3 0.00
102 40 0.06
103 4 0.01
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (93 bp):
AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATG
CTGATTCAAGGCCAGCTATATTGGACTT
Found at i:1238517 original size:141 final size:141
Alignment explanation
Indices: 1238089--1238941 Score: 1003
Period size: 141 Copynumber: 5.9 Consensus size: 141
1238079 GATGAAAAAG
* * * * * * *
1238089 GATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCGATATGC
1 GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT-G---ATGTGCCAATGTGC
* * *
1238154 TGATTCAAGGCCAAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCTAGC
62 TGATTCAAGGCC-AGCTACATTGGACTT--A-A--AAGGTGCCAATGTGCTGATTCAAGGCCAGC
*
1238219 TACATTGGACTTAAAGATAAA
121 TACATTGGACTTAAAGATGAA
* * * * * *
1238240 GGTGCCAATATGCTGATTCAAGGCCAGCTATA-TGGGCTTAATGGTGCAAGTGCCAATGTGCTGA
1 GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG-ATGTGCCAATGTGCTGA
* * *
1238304 GTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATA
65 TTCAAGGCCAGCTACATTGGACTT----A-AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACA
* *
1238369 TTGGACTTAATGGTGAA
125 TTGGACTTAAAGATGAA
* * * * * *
1238386 GGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGATGATGCCAATATGCTGA
1 GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGATG-TGCCAATGTGCTGA
* *
1238451 TTCAAGGCCAGCGATATTGGACTT-AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
65 TTCAAGGCCAGCTACATTGGACTTAAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
1238515 CTTAAAGATGAA
130 CTTAAAGATGAA
* *
1238527 GACGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGATGATGCCAATTTGCTGA
1 GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGATG-TGCCAATGTGCTGA
* *
1238592 TTCAAGGCCAGCGATATTGGACTT-AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
65 TTCAAGGCCAGCTACATTGGACTTAAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
1238656 CTTAAAGATGAA
130 CTTAAAGATGAA
*
1238668 GACGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-G--GTGCCAATGTGCTGAT
1 GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGATGTGCCAATGTGCTGAT
*
1238728 TCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACAT
66 TCAAGGCCAGCTACATTGGACTT--A-A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACAT
*
1238793 TGGACTTAAAGATGAT
126 TGGACTTAAAGATGAA
1238809 GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-G--GTGCCAATGTGCTGAT
1 GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGATGTGCCAATGTGCTGAT
* *
1238869 TCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCTATAT
66 TCAAGGCCAGCTACATTGGACTTAAA-A-G--G-TGCCAATGTGCTGATTCAAGGCCAGCTACAT
*
1238934 TGGGCTTA
126 TGGACTTA
1238942 GAAGGGTTGC
Statistics
Matches: 632, Mismatches: 55, Indels: 40
0.87 0.08 0.06
Matches are distributed among these distances:
135 35 0.06
136 2 0.00
137 1 0.00
138 3 0.00
139 3 0.00
140 3 0.00
141 388 0.61
146 89 0.14
147 67 0.11
148 3 0.00
149 1 0.00
150 9 0.01
151 28 0.04
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (141 bp):
GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGATGTGCCAATGTGCTGAT
TCAAGGCCAGCTACATTGGACTTAAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
TTAAAGATGAA
Found at i:1239024 original size:34 final size:33
Alignment explanation
Indices: 1238941--1239047 Score: 173
Period size: 33 Copynumber: 3.2 Consensus size: 33
1238931 TATTGGGCTT
*
1238941 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTGG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1238974 AAGAA-GGTTGCCACCGACTTGTGTGGGCTTTAG
1 -AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1239007 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGG-TTGCCACCGACTTGTGTGGGCTTTAG
1239041 A-AAGGGT
1 AGAAGGGT
1239048 GAAAGATGCC
Statistics
Matches: 70, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
32 5 0.07
33 34 0.49
34 31 0.44
ACGTcount: A:0.20, C:0.17, G:0.36, T:0.27
Consensus pattern (33 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:1239091 original size:33 final size:33
Alignment explanation
Indices: 1239049--1239681 Score: 493
Period size: 34 Copynumber: 19.6 Consensus size: 33
1239039 AGAAAGGGTG
* * *
1239049 AAAGATGCCACGAAGTTGTGGACTTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAAGAA
* *
1239082 CAAGGTGCCACAGAGTTGTGGGCTTTAAAAAGGAAAA
1 AAAGGTGCCACGGAGTTGTGGGC-TTAAAAA-G--AA
* *
1239119 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
1 AAAG-GTGCCACGGAGTTGTGGGCTTAAAAAGAA
* *
1239153 AAAGAGTGCCACGGAGTTGTGGGCTT-AGAAGGA
1 AAAG-GTGCCACGGAGTTGTGGGCTTAAAAAGAA
* * *
1239186 AAAGAGTGCCACGTAGTTGTGGGCTT-TAAAGGA
1 AAAG-GTGCCACGGAGTTGTGGGCTTAAAAAGAA
* * *
1239219 AAAGAGTGCCACGGAGTCGTGGACTT-AAAAGGA
1 AAAG-GTGCCACGGAGTTGTGGGCTTAAAAAGAA
* *
1239252 AAAGAGTGCCACGGAGTCGTGGACTT-AAAAG--
1 AAAG-GTGCCACGGAGTTGTGGGCTTAAAAAGAA
1239283 ---GGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGC-TTAAAAAGAA
* *
1239314 AAAGTGTGCCACAGAGTTGTGGGCTTTAAACAGAA
1 AAAG-GTGCCACGGAGTTGTGGGC-TTAAAAAGAA
1239349 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGC-TTAAAAAGAA
* *
1239383 AAAGGTGCCACGGAGTTGTGGACTTAAAGATGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAA-AAGAA
* *
1239417 AAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGC-TTAAAAAGAA
* *
1239451 GAAGGTGCCACGGAGTTGTGGGCTT-AAACG--
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAAGAA
* *
1239481 ---GGTGCCACGGAGTTGTGGACTTAAAGATGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAA-AAGAA
* * * *
1239512 AAAAGTGCCACAGAATTGTGGGCTTTAAAAG--
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAAGAA
* *
1239543 ---GGTGCCACGGAGTTGTGGACTTAAAGATGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAA-AAGAA
** * *
1239574 AAAAATGCCACGGAATTGTGGGCTTTAAAAG--
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAAGAA
* *
1239605 ---GGTGCCACGGAATTGTGGGCTTTAAAAG--
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAAGAA
* *
1239633 ---GGTGCCACGGAATTGTGGGCTT-TAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAAGAA
* * *
1239662 AAA-ATGCCACTGAGTCGTGG
1 AAAGGTGCCACGGAGTTGTGG
1239682 ACTTTGAGAC
Statistics
Matches: 505, Mismatches: 62, Indels: 68
0.80 0.10 0.11
Matches are distributed among these distances:
27 42 0.08
28 73 0.14
29 9 0.02
31 13 0.03
32 4 0.01
33 122 0.24
34 176 0.35
35 37 0.07
36 1 0.00
37 10 0.02
38 18 0.04
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.21
Consensus pattern (33 bp):
AAAGGTGCCACGGAGTTGTGGGCTTAAAAAGAA
Found at i:1239289 original size:27 final size:27
Alignment explanation
Indices: 1239218--1239309 Score: 94
Period size: 33 Copynumber: 3.1 Consensus size: 27
1239208 GCTTTAAAGG
*
1239218 AAAAGAGTGCCACGGAGTCGTGGACTT
1 AAAAGGGTGCCACGGAGTCGTGGACTT
1239245 AAAAGGAAAAGAGTGCCACGGAGTCGTGGACTT
1 AAAA-G----G-GTGCCACGGAGTCGTGGACTT
* *
1239278 AAAAGGGTGCCACGGAGTTGTGGGCTTT
1 AAAAGGGTGCCACGGAGTCGTGGAC-TT
1239306 AAAA
1 AAAA
1239310 AGAAAAAGTG
Statistics
Matches: 55, Mismatches: 3, Indels: 13
0.77 0.04 0.18
Matches are distributed among these distances:
27 21 0.38
28 8 0.15
32 1 0.02
33 25 0.45
ACGTcount: A:0.33, C:0.15, G:0.34, T:0.18
Consensus pattern (27 bp):
AAAAGGGTGCCACGGAGTCGTGGACTT
Found at i:1239399 original size:68 final size:62
Alignment explanation
Indices: 1239347--1239658 Score: 327
Period size: 62 Copynumber: 5.0 Consensus size: 62
1239337 CTTTAAACAG
* * *
1239347 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAG
1 AAAAGGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAATTGTGGGCTT----
1239412 AT
62 -T
** * * *
1239414 GAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGC-TT
1 -AAAAGGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAATTGTGGGCTTT
* * * * *
1239476 AAACGGGTGCCACGGAGTTGTGGAC-TTAAAGATGAAAAAAGTGCCACAGAATTGTGGGCTTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTTTAAA-AAGAAAAAGGTGCCACGGAATTGTGGGCTTT
* * **
1239538 AAAAGGGTGCCACGGAGTTGTGGAC-TTAAAGATGAAAAAAATGCCACGGAATTGTGGGCTTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTTTAAA-AAGAAAAAGGTGCCACGGAATTGTGGGCTTT
*
1239600 AAAAGGGTGCCACGGAATTGTGGGCTTT-AAAAG-----GGTGCCACGGAATTGTGGGCTTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAATTGTGGGCTTT
1239656 AAA
1 AAA
1239659 GAAAAAATGC
Statistics
Matches: 219, Mismatches: 22, Indels: 18
0.85 0.08 0.07
Matches are distributed among these distances:
56 24 0.11
60 4 0.02
61 46 0.21
62 87 0.40
63 2 0.01
67 1 0.00
68 55 0.25
ACGTcount: A:0.32, C:0.13, G:0.33, T:0.22
Consensus pattern (62 bp):
AAAAGGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAATTGTGGGCTTT
Found at i:1239486 original size:198 final size:194
Alignment explanation
Indices: 1239085--1239602 Score: 610
Period size: 198 Copynumber: 2.7 Consensus size: 194
1239075 AAAAGAACAA
* *
1239085 GGTGCCACAGAGTTGTGGGCTTTAAAAAGGAAAAAAAGAGTGCCACGGAGTTGTGGGC-TTAGAA
1 GGTGCCACGGAGTTGTGGGCTTTAAAAA-G--AAAAAGAGTGCCACAGAGTTGTGGGCTTTA-AA
* * * * *
1239149 GGAAAAAGAGTGCCACGGAGTTGTGGGCTT-AGAAGGAAAAGAGTGCCACGTAGTTGTGGGCTTT
62 AGAAAAAG-GTGCCACGGAGTTGTGGGCTTAAAAAGAAAAAG-GTGCCACGGAGTTGTGGACTTT
*
1239213 AAAGGAAAAGAGTGCCACGGAGTCGTGGACTTAAAAGGAAAAGAGTGCCACGGAGTCGTGGACTT
125 AAAGGAAAAAAGTGCCACGGAGTCGTGGACTTAAAAGGAAAAGAGTGCCACGGAGTCGTGGACTT
1239278 AAAAG
190 AAAAG
*
1239283 GGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGTGTGCCACAGAGTTGTGGGCTTTAAACAGA
1 GGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAA-AGA
1239348 AAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGAC-TTAAAG
65 AAAAGGTGCCACGGAGTTGTGGGC-TTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTTAAAG
* * * *
1239412 ATGAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAA-GAAGAAG-GTGCCACGGAGTTGTGGGCT
129 --GAAAAAAGTGCCACGGAGTCGTGGAC-TT-AAAAGGAA-AAGAGTGCCACGGAGTCGTGGACT
*
1239475 TAAACG
189 TAAAAG
* * *
1239481 GGTGCCACGGAGTTGTGGAC-TTAAAGATGAAAAA-AGTGCCACAGAATTGTGGGCTTTAAAAG-
1 GGTGCCACGGAGTTGTGGGCTTTAAA-AAGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAGA
* * ** * *
1239543 ----GGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAAATGCCACGGAATTGTGGGCTTTAAA
65 AAAAGGTGCCACGGAGTTGTGGGCTTAAA-AAGAAAAAGGTGCCACGGAGTTGTGGACTTTAAA
1239603 AGGGTGCCAC
Statistics
Matches: 284, Mismatches: 24, Indels: 30
0.84 0.07 0.09
Matches are distributed among these distances:
190 5 0.02
191 42 0.15
192 5 0.02
195 51 0.18
196 31 0.11
197 62 0.22
198 81 0.29
199 7 0.02
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.21
Consensus pattern (194 bp):
GGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAGAA
AAAGGTGCCACGGAGTTGTGGGCTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTTAAAGGA
AAAAAGTGCCACGGAGTCGTGGACTTAAAAGGAAAAGAGTGCCACGGAGTCGTGGACTTAAAAG
Found at i:1239550 original size:28 final size:28
Alignment explanation
Indices: 1239421--1239658 Score: 190
Period size: 28 Copynumber: 7.9 Consensus size: 28
1239411 GATGAAAAAA
*
1239421 GTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAG
1 GTGCCACGGAATTGTGGGCTTT---AA-AAG--G
* *
1239455 GTGCCACGGAGTTGTGGGC-TTAAACGG
1 GTGCCACGGAATTGTGGGCTTTAAAAGG
* * **
1239482 GTGCCACGGAGTTGTGGACTTAAAGATGAAAAAA
1 GTGCCACGGAATTGTGGGCTT-----T-AAAAGG
*
1239516 GTGCCACAGAATTGTGGGCTTTAAAAGG
1 GTGCCACGGAATTGTGGGCTTTAAAAGG
* * **
1239544 GTGCCACGGAGTTGTGGACTTAAAGATGAAAAAA
1 GTGCCACGGAATTGTGGGCTT-----T-AAAAGG
*
1239578 ATGCCACGGAATTGTGGGCTTTAAAAGG
1 GTGCCACGGAATTGTGGGCTTTAAAAGG
1239606 GTGCCACGGAATTGTGGGCTTTAAAAGG
1 GTGCCACGGAATTGTGGGCTTTAAAAGG
1239634 GTGCCACGGAATTGTGGGCTTTAAA
1 GTGCCACGGAATTGTGGGCTTTAAA
1239659 GAAAAAATGC
Statistics
Matches: 170, Mismatches: 21, Indels: 32
0.76 0.09 0.14
Matches are distributed among these distances:
27 19 0.11
28 79 0.46
29 4 0.02
30 2 0.01
33 4 0.02
34 62 0.36
ACGTcount: A:0.29, C:0.14, G:0.34, T:0.23
Consensus pattern (28 bp):
GTGCCACGGAATTGTGGGCTTTAAAAGG
Found at i:1240690 original size:16 final size:16
Alignment explanation
Indices: 1240671--1240702 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1240661 TTTCCTCTCT
*
1240671 TTTTTTTTCTTTTTTG
1 TTTTGTTTCTTTTTTG
1240687 TTTTGTTTCTTTTTTG
1 TTTTGTTTCTTTTTTG
1240703 GAAAAGAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.06, G:0.09, T:0.84
Consensus pattern (16 bp):
TTTTGTTTCTTTTTTG
Found at i:1240965 original size:19 final size:19
Alignment explanation
Indices: 1240943--1241012 Score: 104
Period size: 19 Copynumber: 3.6 Consensus size: 19
1240933 TTGCACTTTC
*
1240943 TTTTTTTTTTTTTTTTTTG
1 TTTTTTTTTTTTTTGTTTG
*
1240962 TTTTTTTTTTTTTTGTGTG
1 TTTTTTTTTTTTTTGTTTG
*
1240981 TTTTTTTTTTGTTTGTTTG
1 TTTTTTTTTTTTTTGTTTG
1241000 TTTGTTTTTTTTT
1 TTT-TTTTTTTTT
1241013 CCATCACCTT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 37 0.82
20 8 0.18
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (19 bp):
TTTTTTTTTTTTTTGTTTG
Found at i:1241026 original size:1 final size:1
Alignment explanation
Indices: 1240943--1241012 Score: 68
Period size: 1 Copynumber: 70.0 Consensus size: 1
1240933 TTGCACTTTC
* * * * * * * *
1240943 TTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTTGTGTGTTTTTTTTTTGTTTGTTTGTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1241008 TTTTT
1 TTTTT
1241013 CCATCACCTT
Statistics
Matches: 53, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (1 bp):
T
Found at i:1247961 original size:52 final size:52
Alignment explanation
Indices: 1247891--1248011 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
1247881 GAAAATTTAT
*
1247891 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
1247943 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
1247995 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
1248012 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:1248024 original size:52 final size:51
Alignment explanation
Indices: 1247891--1248031 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
1247881 GAAAATTTAT
1247891 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
1247943 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
1247995 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
1248032 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:1248038 original size:13 final size:13
Alignment explanation
Indices: 1248020--1248044 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1248010 CAAAGATCAG
1248020 TGTATCGATACAA
1 TGTATCGATACAA
1248033 TGTATCGATACA
1 TGTATCGATACA
1248045 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1248128 original size:13 final size:13
Alignment explanation
Indices: 1248110--1248134 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1248100 CAAAAAAATA
1248110 TGTATCGATACAT
1 TGTATCGATACAT
1248123 TGTATCGATACA
1 TGTATCGATACA
1248135 ACATTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1254859 original size:25 final size:23
Alignment explanation
Indices: 1254831--1254879 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
1254821 AAAAGAAACA
1254831 AAACAAAAAAGGAAAAAAAAAGAAG
1 AAACAAAAAA--AAAAAAAAAGAAG
* *
1254856 AAACAAATAAACAAAAAAAGAAG
1 AAACAAAAAAAAAAAAAAAGAAG
1254879 A
1 A
1254880 GAGGAAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 13 0.59
25 9 0.41
ACGTcount: A:0.80, C:0.06, G:0.12, T:0.02
Consensus pattern (23 bp):
AAACAAAAAAAAAAAAAAAGAAG
Found at i:1255427 original size:33 final size:33
Alignment explanation
Indices: 1255371--1255515 Score: 220
Period size: 33 Copynumber: 4.4 Consensus size: 33
1255361 TTTCATGTCA
*
1255371 GTGGCAACCCTTCTC-AAAGCCCACACAAGTTG
1 GTGGCAACCTTTCTCTAAAGCCCACACAAGTTG
*
1255403 GTGGCAACCTTTTTCTAAAGCCCACACAAGTTG
1 GTGGCAACCTTTCTCTAAAGCCCACACAAGTTG
*
1255436 GTGGCAACCTTTTTCTAAAGCCCACACAAGTTG
1 GTGGCAACCTTTCTCTAAAGCCCACACAAGTTG
* * *
1255469 GTGGCAACCATTCTCTAAAGCCCAAACAAGTCG
1 GTGGCAACCTTTCTCTAAAGCCCACACAAGTTG
*
1255502 GTGGCAACCCTTCT
1 GTGGCAACCTTTCT
1255516 AAGCCCAATA
Statistics
Matches: 105, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 13 0.12
33 92 0.88
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (33 bp):
GTGGCAACCTTTCTCTAAAGCCCACACAAGTTG
Found at i:1255579 original size:49 final size:49
Alignment explanation
Indices: 1255515--1256269 Score: 778
Period size: 49 Copynumber: 15.8 Consensus size: 49
1255505 GCAACCCTTC
* *
1255515 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* * * *
1255564 TAAGACCAATGTCGCTGGCCTTGAATCAGCAAATTAGCA-C-----CTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* * * *
1255607 TAAGTCCAATATCGTTGGCCTTGAATCAGCATATTAGCACTTTTGTCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* * * *
1255656 TAAGTCCAATCTCGCTGGCCTTCAATCAACACATTGGCA-C-----CTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1255699 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* *
1255748 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC----TC--
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* * *
1255791 CAAGTCTAATATCGCTGGTCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* * * *
1255840 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATCGGCA-C-----CTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1255883 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* * * *
1255932 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATCGGCA-C-----CTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
**
1255975 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGTGCCTTTGTCATCTTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TT-T-ATC-TT
* * * *
1256028 TAAGTCCAATGTCGCTGGCCTTGAATCAACACATTGGCACCTTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
*
1256077 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TT-T-ATCTT
* * * *
1256129 TAAGTCCAATGTCGCTGGCTTTGAATCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* * *
1256178 TAGGTCCAGTATCGCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT--T-ATCTT
** * * * *
1256230 TAAAACCCAATGTCGTTGGCCTTTAATCAGCACATTGGCA
1 T-AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
1256270 TTCTTCTCAT
Statistics
Matches: 585, Mismatches: 80, Indels: 78
0.79 0.11 0.10
Matches are distributed among these distances:
43 186 0.32
44 3 0.01
45 2 0.00
47 2 0.00
48 3 0.01
49 264 0.45
50 5 0.01
51 2 0.00
52 51 0.09
53 67 0.11
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (49 bp):
TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
Found at i:1255677 original size:92 final size:92
Alignment explanation
Indices: 1255510--1256269 Score: 998
Period size: 92 Copynumber: 8.0 Consensus size: 92
1255500 CGGTGGCAAC
* * *
1255510 CCTTCTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATG
1 CCTT-TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATG
* *
1255575 TCGCTGGCCTTGAATCAGCAAATTAGCA
65 TCGCTGGCCTTGAATCAGCACATTGGCA
* * * * *
1255603 CCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTAGCACTTTTGTCTTTAAGTCCAATCT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGT
* *
1255668 CGCTGGCCTTCAATCAACACATTGGCA
66 CGCTGGCCTTGAATCAGCACATTGGCA
*
1255695 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATAT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGT
*
1255760 AGCTGGCCTTGAATCAGCACATTGGCA
66 CGCTGGCCTTGAATCAGCACATTGGCA
** * *
1255787 CCTCCAAGTCTAATATCGCTGGTCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGT
* *
1255852 AGCTGGCCTTGAATCAGCACATCGGCA
66 CGCTGGCCTTGAATCAGCACATTGGCA
1255879 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGT
* *
1255944 AGCTGGCCTTGAATCAGCACATCGGCA
66 CGCTGGCCTTGAATCAGCACATTGGCA
**
1255971 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGTGCCTTTGTCATCTTTTAAGTCCA
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TT-T-ATC-TTTAAGTCCA
*
1256036 ATGTCGCTGGCCTTGAATCAACACATTGGCA
62 ATGTCGCTGGCCTTGAATCAGCACATTGGCA
*
1256067 CCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAA
1 ----C--CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TT-T-ATCTTTAA
*
1256132 GTCCAATGTCGCTGGCTTTGAATCAGCACATTGGCA
57 GTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
* * *
1256168 CCTTCATCTTTAGGTCCAGTATCGCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAA
1 ----C--CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT--T-ATCTTT-A
** * *
1256233 AACCCAATGTCGTTGGCCTTTAATCAGCACATTGGCA
56 AGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
1256270 TTCTTCTCAT
Statistics
Matches: 612, Mismatches: 43, Indels: 15
0.91 0.06 0.02
Matches are distributed among these distances:
92 379 0.62
93 6 0.01
94 1 0.00
95 3 0.00
96 38 0.06
100 3 0.00
101 97 0.16
102 85 0.14
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (92 bp):
CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGT
CGCTGGCCTTGAATCAGCACATTGGCA
Found at i:1255720 original size:22 final size:22
Alignment explanation
Indices: 1255653--1255720 Score: 52
Period size: 22 Copynumber: 3.1 Consensus size: 22
1255643 GCACTTTTGT
*
1255653 CTTTAAGTCCAATCTCGCTGGC
1 CTTTAAGTCCAATATCGCTGGC
* * **
1255675 CTTCAA-T-CAACA-CATTGGCAC
1 CTTTAAGTCCAATATCGCTGG--C
1255696 CTTTAAGTCCAATATCGCTGGC
1 CTTTAAGTCCAATATCGCTGGC
1255718 CTT
1 CTT
1255721 GAATCAGCAT
Statistics
Matches: 32, Mismatches: 9, Indels: 10
0.63 0.18 0.20
Matches are distributed among these distances:
19 4 0.12
20 3 0.09
21 7 0.22
22 10 0.31
23 4 0.12
24 4 0.12
ACGTcount: A:0.24, C:0.31, G:0.15, T:0.31
Consensus pattern (22 bp):
CTTTAAGTCCAATATCGCTGGC
Found at i:1257061 original size:32 final size:32
Alignment explanation
Indices: 1257020--1257095 Score: 111
Period size: 32 Copynumber: 2.4 Consensus size: 32
1257010 TTCAACGATT
1257020 TGTATCGATACATAAGTGTTATGT-T-GATACAA
1 TGTATCGATACATAAGT-TT-TGTATCGATACAA
1257052 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTTTTGTATCGATACAA
*
1257084 TGTATCGCTACA
1 TGTATCGATACA
1257096 AAGCTACTGC
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
30 3 0.07
31 3 0.07
32 35 0.85
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTTTTGTATCGATACAA
Found at i:1257153 original size:13 final size:13
Alignment explanation
Indices: 1257135--1257159 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1257125 ATTACTCAAA
1257135 TGTATCGATACAT
1 TGTATCGATACAT
1257148 TGTATCGATACA
1 TGTATCGATACA
1257160 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1257213 original size:52 final size:51
Alignment explanation
Indices: 1257148--1257276 Score: 172
Period size: 52 Copynumber: 2.5 Consensus size: 51
1257138 ATCGATACAT
*
1257148 TGTATCGATACACTGATCT-TTGTATCGATACATG-CAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-AT-TAATGTATCGATACA-GACAGGCAAATTTGCCCAGA
*
1257200 TGTATCGACACACTATTAAATGTATCGATACAGACAGGCAAATTTGCCCAGA
1 TGTATCGATACACTATT-AATGTATCGATACAGACAGGCAAATTTGCCCAGA
*
1257252 TGTATCGATACACTATGAAATGTAT
1 TGTATCGATACACTAT-TAATGTAT
1257277 AAATACATGC
Statistics
Matches: 69, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
50 1 0.01
51 3 0.04
52 65 0.94
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.29
Consensus pattern (51 bp):
TGTATCGATACACTATTAATGTATCGATACAGACAGGCAAATTTGCCCAGA
Found at i:1257283 original size:52 final size:52
Alignment explanation
Indices: 1257175--1257296 Score: 183
Period size: 52 Copynumber: 2.3 Consensus size: 52
1257165 CTTTGTATCG
* **
1257175 ATACATGCAGGCAAATTTGCCCAGATGTATCGACACACTATTAAATGTATCG
1 ATACATGCAGGCAAATTTGCCCAGATGTATCGACACACTATGAAATGTATAA
*
1257227 ATACA-GACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATGTATAA
1 ATACATG-CAGGCAAATTTGCCCAGATGTATCGACACACTATGAAATGTATAA
*
1257279 ATACATGCAAGCAAATTT
1 ATACATGCAGGCAAATTT
1257297 TCATATTTCA
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
51 1 0.02
52 61 0.97
53 1 0.02
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (52 bp):
ATACATGCAGGCAAATTTGCCCAGATGTATCGACACACTATGAAATGTATAA
Found at i:1264491 original size:17 final size:16
Alignment explanation
Indices: 1264465--1264522 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
1264455 GTTCTTTTCC
*
1264465 AAAAAAGAAACAAAACG
1 AAAAAAGAAA-AAAAAG
*
1264482 AAAAAGGAAAAAAAAG
1 AAAAAAGAAAAAAAAG
* *
1264498 AAAAAACAAACAAACA-
1 AAAAAAGAAA-AAAAAG
1264514 AAAAAAGAA
1 AAAAAAGAA
1264523 GAGAGGAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
16 21 0.62
17 13 0.38
ACGTcount: A:0.81, C:0.09, G:0.10, T:0.00
Consensus pattern (16 bp):
AAAAAAGAAAAAAAAG
Found at i:1265365 original size:16 final size:17
Alignment explanation
Indices: 1265340--1265377 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1265330 TTGTGCTGTA
* *
1265340 ATCATGACATC-ATGAC
1 ATCATAACATCAATAAC
1265356 ATCATAACATCAATAAC
1 ATCATAACATCAATAAC
1265373 ATCAT
1 ATCAT
1265378 TATTTGCATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.45, C:0.24, G:0.05, T:0.26
Consensus pattern (17 bp):
ATCATAACATCAATAAC
Found at i:1265612 original size:31 final size:30
Alignment explanation
Indices: 1265472--1265789 Score: 286
Period size: 31 Copynumber: 10.1 Consensus size: 30
1265462 AATTCTTCAA
*
1265472 ATCTCTTC-TCAAAGCCCACGACTCAGTGGC
1 ATCT-TTCTTCAAAGTCCACGACTCAGTGGC
* * *
1265502 ATCTTTCCTTCTTAAAGTCAATGACTTAGTGGC
1 ATCTTT-CTTC--AAAGTCCACGACTCAGTGGC
* *
1265535 ATCTTGTC-TCAAAGTCCACAATTCAGTGGC
1 ATCTT-TCTTCAAAGTCCACGACTCAGTGGC
*
1265565 ATCTCTT-TCCAAAGTCCACGACTCAGTGGC
1 ATCT-TTCTTCAAAGTCCACGACTCAGTGGC
*
1265595 ATCTATTCTTCAAAGTCCACGACTCTGTGGC
1 ATCT-TTCTTCAAAGTCCACGACTCAGTGGC
* *
1265626 ACCTTTTTCATTTCAAAGTCCACGACTCCGTGGC
1 A--TCTTTC--TTCAAAGTCCACGACTCAGTGGC
*
1265660 A-CCTTCTTTCCAAAGTCCACGACTCAGTGGC
1 ATCTTTC-TT-CAAAGTCCACGACTCAGTGGC
*
1265691 ATCTTTTCTTCAAAGTCCACGACTCCGTGGC
1 ATC-TTTCTTCAAAGTCCACGACTCAGTGGC
*
1265722 ACCTTTTTCTTTTCAAAGTCCACGACTTC-GTGGC
1 A--TCTTTC--TTCAAAGTCCACGAC-TCAGTGGC
* *
1265756 ACCTTCTTTTCAAAGTCCACGACTCAGTGGC
1 ATCTT-TCTTCAAAGTCCACGACTCAGTGGC
1265787 ATC
1 ATC
1265790 AAAGTCCACG
Statistics
Matches: 239, Mismatches: 27, Indels: 43
0.77 0.09 0.14
Matches are distributed among these distances:
29 2 0.01
30 55 0.23
31 92 0.38
32 14 0.06
33 29 0.12
34 45 0.19
35 2 0.01
ACGTcount: A:0.22, C:0.31, G:0.16, T:0.31
Consensus pattern (30 bp):
ATCTTTCTTCAAAGTCCACGACTCAGTGGC
Found at i:1265795 original size:23 final size:23
Alignment explanation
Indices: 1265765--1265810 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
1265755 CACCTTCTTT
1265765 TCAAAGTCCACGACTCAGTGGCA
1 TCAAAGTCCACGACTCAGTGGCA
*
1265788 TCAAAGTCCACGACTCCGTGGCA
1 TCAAAGTCCACGACTCAGTGGCA
1265811 CCTTTTTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.28, C:0.33, G:0.22, T:0.17
Consensus pattern (23 bp):
TCAAAGTCCACGACTCAGTGGCA
Found at i:1266316 original size:100 final size:100
Alignment explanation
Indices: 1265790--1266646 Score: 1457
Period size: 100 Copynumber: 8.5 Consensus size: 100
1265780 CAGTGGCATC
* * * *
1265790 AAAGTCCACGACTCCGTGGCACCTT-TTTCTTTTAAGTCCACGACTCCATGGCACCTTCTTTTCA
1 AAAGTCCACAACCCCGTGGCACCTTGTTCCTTTTAAGTCCACGACTCCGTGGCACCTTCTTTTCA
* * *
1265854 AAACCCACAACAT-CATAGCACTCTTTTTTCCCTTTT
66 AAGCCCACAAC-TCCGTGGCACTC-TTTTTCCCTTTT
1265890 AAAGTCCACAACCCCGTGGCACCTTGTTCCTTTTAAGTCCACGACTCCGTGGCACCTTCTTTTCA
1 AAAGTCCACAACCCCGTGGCACCTTGTTCCTTTTAAGTCCACGACTCCGTGGCACCTTCTTTTCA
1265955 AAGCCCACAACTCCGTGGCACTCTTTTTTCCCTTTT
66 AAGCCCACAACTCCGTGGCACTC-TTTTTCCCTTTT
* *
1265991 AAAGTCCAAAACCCCGTGGCACCTTGTTCTTTTTAAGTCCACGACTCCGTGGCACCTTCTTTTCA
1 AAAGTCCACAACCCCGTGGCACCTTGTTCCTTTTAAGTCCACGACTCCGTGGCACCTTCTTTTCA
1266056 AAGCCCACAACTCCGTGGCACTCTTTTTTCCCTTTT
66 AAGCCCACAACTCCGTGGCACTC-TTTTTCCCTTTT
1266092 AAAGTCCACAACCCCGTGGCACCTTGTTCCTTTTAAGTCCACGACTCCGTGGCACCTTCTTTTCA
1 AAAGTCCACAACCCCGTGGCACCTTGTTCCTTTTAAGTCCACGACTCCGTGGCACCTTCTTTTCA
* *
1266157 AAGCCCATAACTCTGTGGCACTCTTCTTTCCCTTTT
66 AAGCCCACAACTCCGTGGCACTCTT-TTTCCCTTTT
*
1266193 AAAGTCCACAACCCCGTGGCACCTTGTTCTTTTTAAGTCCACGACTCCGTGGCACCTTCTTTTCA
1 AAAGTCCACAACCCCGTGGCACCTTGTTCCTTTTAAGTCCACGACTCCGTGGCACCTTCTTTTCA
*
1266258 AAGCCCACAACTCCGCGGCACTCTTTTTCCCTTTT
66 AAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
*
1266293 AAAGTCCACAACCCCGTGGCACCTTGTTCCTTTTAAGTCCAGGACTCCGTGGCACCTTCTTTTCA
1 AAAGTCCACAACCCCGTGGCACCTTGTTCCTTTTAAGTCCACGACTCCGTGGCACCTTCTTTTCA
1266358 AAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
66 AAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
* *
1266393 AAAGTCCACAACCCCGTGGCACCTTGTTCTTTTTAAGTCCACAACTCCGTGGCACCTTCTTTTCA
1 AAAGTCCACAACCCCGTGGCACCTTGTTCCTTTTAAGTCCACGACTCCGTGGCACCTTCTTTTCA
1266458 AAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
66 AAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
1266493 AAAGTCCACAACCCCGTGGCACCTTGTTCCTTTTAAGTCCACGACTCCGTGGCACCTTCTTTTCA
1 AAAGTCCACAACCCCGTGGCACCTTGTTCCTTTTAAGTCCACGACTCCGTGGCACCTTCTTTTCA
*
1266558 AAGCCCACAACTTCGTGGCACTCTTTTTCCCTTTT
66 AAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
** * * *
1266593 AAAGTCCACAACTTCATGGCACCTTGTTCCTTTTAAGTCCACAACTTCGTGGCA
1 AAAGTCCACAACCCCGTGGCACCTTGTTCCTTTTAAGTCCACGACTCCGTGGCA
1266647 TTTTCCACCA
Statistics
Matches: 723, Mismatches: 31, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
100 376 0.52
101 347 0.48
ACGTcount: A:0.20, C:0.34, G:0.14, T:0.32
Consensus pattern (100 bp):
AAAGTCCACAACCCCGTGGCACCTTGTTCCTTTTAAGTCCACGACTCCGTGGCACCTTCTTTTCA
AAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
Found at i:1266702 original size:32 final size:32
Alignment explanation
Indices: 1266661--1266820 Score: 178
Period size: 33 Copynumber: 4.9 Consensus size: 32
1266651 CCACCATTTT
1266661 CAAAGCCCACACAAGTCGGTGGCAACCCTTTC
1 CAAAGCCCACACAAGTCGGTGGCAACCCTTTC
* * *
1266693 CAAACCCCACATAAGTCAGTGGCAACCC-TTC
1 CAAAGCCCACACAAGTCGGTGGCAACCCTTTC
* **
1266724 TCAAAGCCCACACAAGTTGGTGGCAACTTTTTTC
1 -CAAAGCCCACACAAGTCGGTGGCAAC-CCTTTC
* * *
1266758 TAAAGCCCACACAAGTTGGTGGCAACCATTCTC
1 CAAAGCCCACACAAGTCGGTGGCAACCCTT-TC
* * *
1266791 TAAAGCGCACACAAATCGGTGGCAACCCTT
1 CAAAGCCCACACAAGTCGGTGGCAACCCTT
1266821 CTAAGCCCAA
Statistics
Matches: 108, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
31 3 0.03
32 49 0.45
33 53 0.49
34 3 0.03
ACGTcount: A:0.30, C:0.33, G:0.17, T:0.20
Consensus pattern (32 bp):
CAAAGCCCACACAAGTCGGTGGCAACCCTTTC
Found at i:1266729 original size:64 final size:64
Alignment explanation
Indices: 1266653--1266820 Score: 210
Period size: 65 Copynumber: 2.6 Consensus size: 64
1266643 GGCATTTTCC
* *
1266653 ACCATTTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTCCAAACCCCACATAAGTCAGTGGCA
1 ACCATTCTCAAAGCCCACACAAGTCGGTGGCAACCCTTTCCAAACCCCACACAAGTCAGTGGCA
* * ** * * **
1266717 ACCCTTCTCAAAGCCCACACAAGTTGGTGGCAACTTTTTTCTAAAGCCCACACAAGTTGGTGGCA
1 ACCATTCTCAAAGCCCACACAAGTCGGTGGCAAC-CCTTTCCAAACCCCACACAAGTCAGTGGCA
* *
1266782 ACCATTCTCTAAAGCGCACACAAATCGGTGGCAACCCTT
1 ACCATTCTC-AAAGCCCACACAAGTCGGTGGCAACCCTT
1266821 CTAAGCCCAA
Statistics
Matches: 86, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
64 31 0.36
65 33 0.38
66 22 0.26
ACGTcount: A:0.30, C:0.32, G:0.17, T:0.21
Consensus pattern (64 bp):
ACCATTCTCAAAGCCCACACAAGTCGGTGGCAACCCTTTCCAAACCCCACACAAGTCAGTGGCA
Found at i:1266767 original size:33 final size:32
Alignment explanation
Indices: 1266657--1266820 Score: 193
Period size: 32 Copynumber: 5.1 Consensus size: 32
1266647 TTTTCCACCA
1266657 TTTTCAAAGCCCACACAAGTCGGTGGCAACCC
1 TTTTCAAAGCCCACACAAGTCGGTGGCAACCC
* * * *
1266689 TTTCCAAACCCCACATAAGTCAGTGGCAACCC
1 TTTTCAAAGCCCACACAAGTCGGTGGCAACCC
* * **
1266721 TTCTCAAAGCCCACACAAGTTGGTGGCAACTT
1 TTTTCAAAGCCCACACAAGTCGGTGGCAACCC
* *
1266753 TTTTCTAAAGCCCACACAAGTTGGTGGCAACCA
1 TTTTC-AAAGCCCACACAAGTCGGTGGCAACCC
* * *
1266786 TTCTCTAAAGCGCACACAAATCGGTGGCAACCC
1 TTTTC-AAAGCCCACACAAGTCGGTGGCAACCC
1266819 TT
1 TT
1266821 CTAAGCCCAA
Statistics
Matches: 111, Mismatches: 20, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
32 56 0.50
33 55 0.50
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.22
Consensus pattern (32 bp):
TTTTCAAAGCCCACACAAGTCGGTGGCAACCC
Found at i:1266888 original size:49 final size:49
Alignment explanation
Indices: 1266822--1267668 Score: 868
Period size: 49 Copynumber: 17.8 Consensus size: 49
1266812 GCAACCCTTC
* *
1266822 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* * * * *
1266871 TAAGACCAATGTTGCTGGCCTTGAATCAGCACATTAGCA-C-----CTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* *
1266914 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTTGTCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* *
1266963 TAAGTCCAATCTCGCTGGCCTTGAATCAGCACATTGGCA-C-----CTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* *
1267006 TAAGTCCAATATCGATGGCCTTGAATCAGCATATTGGCACCATTATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* * * *
1267055 TAAGACCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC----TC--
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
*
1267098 CAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* * * * *
1267147 TAAGTCTAATGTAGCTGGCCTTGAATCAGCACATCGGCA-C-----CTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
*
1267190 TAAGTCCATTATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* * * * * *
1267239 TAAGTCCAATGTAGCTGGCCTTCAATTAGCACATCGGCA-C-----CTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
*
1267282 TAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* * *
1267331 TAAGTCCAATGTAGCTGGCCTTGAATCAGCATATCGGCA-C-----CTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
*
1267374 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TT-T-ATC-TT
* * * *
1267427 TAAGTCCAATGTCGCTGGTCTTGAATCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* *
1267476 TAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCGCCTTTGTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TT-T-ATCTT
* * *
1267528 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* *
1267577 TAAGTCCAGTATCGCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT--T-ATCTT
** * * *
1267629 TAAAACCCAATGTCGTTGGCCTAT-AATCAGCACATTGGCA
1 T-AAGTCCAATATCGCTGGCCT-TGAATCAGCATATTGGCA
1267669 TTCTTCTCAT
Statistics
Matches: 661, Mismatches: 89, Indels: 92
0.79 0.11 0.11
Matches are distributed among these distances:
43 221 0.33
44 4 0.01
45 2 0.00
47 2 0.00
48 4 0.01
49 301 0.46
50 5 0.01
51 2 0.00
52 51 0.08
53 68 0.10
54 1 0.00
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (49 bp):
TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
Found at i:1266984 original size:92 final size:92
Alignment explanation
Indices: 1266817--1267668 Score: 1157
Period size: 92 Copynumber: 9.0 Consensus size: 92
1266807 CGGTGGCAAC
* * *
1266817 CCTTCTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATG
1 CCTT-TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATG
* *
1266882 TTGCTGGCCTTGAATCAGCACATTAGCA
65 TAGCTGGCCTTGAATCAGCACATTGGCA
* * *
1266910 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTTGTCTTTAAGTCCAATCT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGT
*
1266975 CGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* * *
1267002 CCTTTAAGTCCAATATCGATGGCCTTGAATCAGCATATTGGCACCATTATCTTTAAGACCAATGT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGT
1267067 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
** *
1267094 CCTCCAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCTAATGT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGT
*
1267159 AGCTGGCCTTGAATCAGCACATCGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
*
1267186 CCTTTAAGTCCATTATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGT
* * *
1267251 AGCTGGCCTTCAATTAGCACATCGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
*
1267278 CCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGT
* *
1267343 AGCTGGCCTTGAATCAGCATATCGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
*
1267370 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTTAAGTCCA
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TT-T-ATC-TTTAAGTCCA
* *
1267435 ATGTCGCTGGTCTTGAATCAGCACATTGGCA
62 ATGTAGCTGGCCTTGAATCAGCACATTGGCA
* *
1267466 CCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCGCCTTTGTCATCTTTAA
1 ----C--CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TT-T-ATCTTTAA
*
1267531 GTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
57 GTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA
* *
1267567 CCTTCATCTTTAAGTCCAGTATCGCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAA
1 ----C--CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT--T-ATCTTT-A
** * *
1267632 AACCCAATGTCGTTGGCCTAT-AATCAGCACATTGGCA
56 AGTCCAATGTAGCTGGCCT-TGAATCAGCACATTGGCA
1267669 TTCTTCTCAT
Statistics
Matches: 702, Mismatches: 44, Indels: 17
0.92 0.06 0.02
Matches are distributed among these distances:
92 468 0.67
93 6 0.01
94 1 0.00
95 3 0.00
96 37 0.05
100 3 0.00
101 98 0.14
102 85 0.12
103 1 0.00
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (92 bp):
CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGT
AGCTGGCCTTGAATCAGCACATTGGCA
Found at i:1267407 original size:22 final size:22
Alignment explanation
Indices: 1267344--1267407 Score: 55
Period size: 21 Copynumber: 3.0 Consensus size: 22
1267334 GTCCAATGTA
1267344 GCTGGCCTTGAATCAGCATATC
1 GCTGGCCTTGAATCAGCATATC
* *
1267366 G--GCACCTTTAAGTC--CAATATC
1 GCTG-GCCTTGAA-TCAGC-ATATC
1267387 GCTGGCCTTGAATCAGCATAT
1 GCTGGCCTTGAATCAGCATAT
1267408 TGGCGCCTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 14
0.63 0.08 0.29
Matches are distributed among these distances:
20 2 0.06
21 14 0.45
22 13 0.42
23 2 0.06
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (22 bp):
GCTGGCCTTGAATCAGCATATC
Found at i:1267679 original size:53 final size:50
Alignment explanation
Indices: 1267379--1267766 Score: 278
Period size: 52 Copynumber: 7.5 Consensus size: 50
1267369 ACCTTTAAGT
* * * * **
1267379 CCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGC-AC-TTCTCATC-TTTAAAC
* * **
1267432 CCAATGTCGCTGGTCTTGAATCAGCACATTGGCACCT-TCATCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTCTCATCTTTAAAC
* * * * * **
1267481 CCAATATCGCTGGCCTTGAATCAACATATTGGCGCCTTTGTCATCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGC-AC-TTCTCATCTTTAAAC
* **
1267533 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCT-TCATCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTCTCATCTTTAAAC
* * * *
1267582 CCAGTATCGCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAAAC
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGC-ACTTC-TCATCTTT-AAAC
* * **
1267635 CCAATGTCGTTGGCCTAT-AATCAGCACATTGGCATTCTTCTCATCTTCAAGT
1 CCAATGTCGCTGGCCT-TGAATCAGCACATTGGCA--CTTCTCATCTTTAAAC
* * * * *
1267687 CTAATGTCGCTGACCGTGAATTAGCACATTGACATCCTTTTTCTCATCTTTAAAC
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCA--C---TTCTCATCTTTAAAC
* * * *
1267742 CCAATATCGTTGGCCGTAAATCAGC
1 CCAATGTCGCTGGCCTTGAATCAGC
1267767 GTATTGGTCC
Statistics
Matches: 274, Mismatches: 47, Indels: 26
0.79 0.14 0.07
Matches are distributed among these distances:
49 78 0.28
50 9 0.03
51 4 0.01
52 81 0.30
53 66 0.24
54 5 0.02
55 31 0.11
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (50 bp):
CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTCTCATCTTTAAAC
Found at i:1268442 original size:19 final size:18
Alignment explanation
Indices: 1268417--1268481 Score: 77
Period size: 19 Copynumber: 3.8 Consensus size: 18
1268407 ATTTCAACGA
1268417 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1268435 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
1268451 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1268467 TTTTGTATCGATACA
1 -TTTGTATCGATACA
1268482 ATGTATCGCT
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
13 11 0.28
15 2 0.05
17 2 0.05
18 1 0.03
19 24 0.60
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.38
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:1268455 original size:32 final size:32
Alignment explanation
Indices: 1268419--1268494 Score: 134
Period size: 32 Copynumber: 2.4 Consensus size: 32
1268409 TTCAACGATT
1268419 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
1268451 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
1268483 TGTATCGCTACA
1 TGTATCGATACA
1268495 AAGCTACTGC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1268456 original size:13 final size:13
Alignment explanation
Indices: 1268438--1268495 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
1268428 ACATAAGTGT
1268438 TGTATCGATACAA
1 TGTATCGATACAA
1268451 TGTATCGATACATAA
1 TGTATCGATAC--AA
1268466 GTTTTGTATCGATACAA
1 ----TGTATCGATACAA
*
1268483 TGTATCGCTACAA
1 TGTATCGATACAA
1268496 AGCTACTGCC
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1268552 original size:13 final size:13
Alignment explanation
Indices: 1268534--1268558 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1268524 ATTACTCAAA
1268534 TGTATCGATACAT
1 TGTATCGATACAT
1268547 TGTATCGATACA
1 TGTATCGATACA
1268559 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1268623 original size:20 final size:20
Alignment explanation
Indices: 1268598--1268650 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
1268588 ATTTGCCCAG
*
1268598 ATGTATCGATACTCTATGAA
1 ATGTATCGATACACTATGAA
1268618 ATGTATCGATACACTATGAA
1 ATGTATCGATACACTATGAA
1268638 ATGTATCGATACA
1 ATGTATCGATACA
1268651 TGCAGGCAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (20 bp):
ATGTATCGATACACTATGAA
Found at i:1274024 original size:14 final size:15
Alignment explanation
Indices: 1274005--1274035 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1273995 TGATTGTTTA
1274005 TTATTTTTTTAT-TT
1 TTATTTTTTTATCTT
1274019 TTATTTTTTTATCTT
1 TTATTTTTTTATCTT
1274034 TT
1 TT
1274036 TTAATTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.84
Consensus pattern (15 bp):
TTATTTTTTTATCTT
Found at i:1274547 original size:20 final size:19
Alignment explanation
Indices: 1274522--1274577 Score: 62
Period size: 18 Copynumber: 2.9 Consensus size: 19
1274512 ATATTTTTTA
*
1274522 TATATTTATTTATTAAAATC
1 TATATTTATATA-TAAAATC
1274542 TATATTTATATATAAAAT-
1 TATATTTATATATAAAATC
*
1274560 TA-ATTTGTTATATAAAAT
1 TATATTT-ATATATAAAAT
1274578 TAATTTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 4 0.12
18 12 0.36
19 6 0.18
20 11 0.33
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (19 bp):
TATATTTATATATAAAATC
Found at i:1276506 original size:32 final size:32
Alignment explanation
Indices: 1276470--1276569 Score: 173
Period size: 32 Copynumber: 3.1 Consensus size: 32
1276460 TTCAACGATT
*
1276470 TGTATCAATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
1276502 TGTATCGATATATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
1276534 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1276566 TGTA
1 TGTA
1276570 AGCTACTGCC
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 64 1.00
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1276507 original size:13 final size:13
Alignment explanation
Indices: 1276489--1276545 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
1276479 ACATAAGTGT
1276489 TGTATCGATACAA
1 TGTATCGATACAA
*
1276502 TGTATCGATATATAA
1 TGTATCG--ATACAA
1276517 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
1276534 TGTATCGATACA
1 TGTATCGATACA
1276546 TAAGTTTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 19 0.53
15 5 0.14
17 5 0.14
19 7 0.19
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1276558 original size:19 final size:18
Alignment explanation
Indices: 1276468--1276564 Score: 79
Period size: 19 Copynumber: 5.8 Consensus size: 18
1276458 ATTTCAACGA
*
1276468 TTTGTATCAATACATAAG
1 TTTGTATCGATACATAAG
1276486 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
*
1276502 --TGTATCGATATATAAG
1 TTTGTATCGATACATAAG
1276518 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
1276534 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1276550 TTTTGTATCGATACA
1 -TTTGTATCGATACA
1276565 ATGTAAGCTA
Statistics
Matches: 63, Mismatches: 3, Indels: 25
0.69 0.03 0.27
Matches are distributed among these distances:
13 21 0.33
15 4 0.06
17 4 0.06
18 1 0.02
19 33 0.52
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.38
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:1276625 original size:13 final size:13
Alignment explanation
Indices: 1276607--1276631 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1276597 ATTACTCAAA
1276607 TGTATCGATACAT
1 TGTATCGATACAT
1276620 TGTATCGATACA
1 TGTATCGATACA
1276632 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1276684 original size:52 final size:52
Alignment explanation
Indices: 1276640--1276768 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
1276630 CACTGATCTT
1276640 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
1276692 TGTATCGATACATGCAGGCAAATCTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1276744 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1276769 TCATATTTCG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1281588 original size:12 final size:12
Alignment explanation
Indices: 1281571--1281601 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1281561 AATTCTTAAT
1281571 TTGAACTCGAAC
1 TTGAACTCGAAC
1281583 TTGAACTCGAAC
1 TTGAACTCGAAC
*
1281595 TCGAACT
1 TTGAACT
1281602 TGAAGTTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAACTCGAAC
Found at i:1282809 original size:22 final size:22
Alignment explanation
Indices: 1282781--1282822 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
1282771 GTCATTGCAC
1282781 TTAAATTTTATTAATTTTTTTT
1 TTAAATTTTATTAATTTTTTTT
1282803 TTAAATTTTATTAATTTTTT
1 TTAAATTTTATTAATTTTTT
1282823 ATTATGCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (22 bp):
TTAAATTTTATTAATTTTTTTT
Found at i:1282834 original size:22 final size:22
Alignment explanation
Indices: 1282782--1282827 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
1282772 TCATTGCACT
*
1282782 TAAATTTTATTAATTTTTTTTT
1 TAAATTTTATTAATTTTTTTTA
1282804 TAAATTTTATTAATTTTTTATTA
1 TAAATTTTATTAATTTTTT-TTA
1282827 T
1 T
1282828 GCTTTTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (22 bp):
TAAATTTTATTAATTTTTTTTA
Found at i:1283580 original size:22 final size:24
Alignment explanation
Indices: 1283545--1283591 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 24
1283535 TCATTGAGCG
*
1283545 TATATCTAATATATATAATTTTAA
1 TATATCTAATATATAAAATTTTAA
1283569 TATATC-AA-ATATAAAATTTTAA
1 TATATCTAATATATAAAATTTTAA
1283591 T
1 T
1283592 TTATTGTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.64
23 2 0.09
24 6 0.27
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (24 bp):
TATATCTAATATATAAAATTTTAA
Found at i:1283620 original size:18 final size:19
Alignment explanation
Indices: 1283594--1283629 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1283584 ATTTTAATTT
*
1283594 ATTGTCATATAT-TATATG
1 ATTGGCATATATATATATG
1283612 ATTGGCATATATATATAT
1 ATTGGCATATATATATAT
1283630 ATATATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.36, C:0.06, G:0.11, T:0.47
Consensus pattern (19 bp):
ATTGGCATATATATATATG
Found at i:1283623 original size:2 final size:2
Alignment explanation
Indices: 1283618--1283651 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1283608 TATGATTGGC
1283618 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1283652 GATGCGAGCC
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1287544 original size:20 final size:20
Alignment explanation
Indices: 1287498--1287544 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1287488 CATTTAGGGA
*
1287498 TGTATCGATACATTTTGTAT
1 TGTATCGATACATTTTGCAT
*
1287518 TGCATCGATACATTTT-CAT
1 TGTATCGATACATTTTGCAT
1287537 GTGTATCG
1 -TGTATCG
1287545 TTATAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.23, C:0.15, G:0.17, T:0.45
Consensus pattern (20 bp):
TGTATCGATACATTTTGCAT
Found at i:1287635 original size:93 final size:92
Alignment explanation
Indices: 1287525--1287715 Score: 219
Period size: 92 Copynumber: 2.1 Consensus size: 92
1287515 TATTGCATCG
** *
1287525 ATACATTTTCATGTGTATCGTTATAAAT-AAGGCTTTCAGAATTT-GTTTAGCTACTACCAACCA
1 ATACATTTTCATGTGTATCAATAAAAATAAAGG-TTTCAGAATTTCG--TAGCTACTACCAACCA
*
1287588 AATGTATCAATACATTCA-AATAATGTATCA
63 AATGTATCAATACATGCACAA-AATGTATCA
** * *
1287618 ATACATTTTCACT-TGTATCAATAAAAATAAAGGTTTCATCATTTCGTAGCTACTACTAACCATA
1 ATACATTTTCA-TGTGTATCAATAAAAATAAAGGTTTCAGAATTTCGTAGCTACTACCAACCAAA
**
1287682 TGTATTGATACATGCACAAAATGTATCA
65 TGTATCAATACATGCACAAAATGTATCA
1287710 ATACAT
1 ATACAT
1287716 GCACAAAATG
Statistics
Matches: 84, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
92 44 0.52
93 34 0.40
94 6 0.07
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.36
Consensus pattern (92 bp):
ATACATTTTCATGTGTATCAATAAAAATAAAGGTTTCAGAATTTCGTAGCTACTACCAACCAAAT
GTATCAATACATGCACAAAATGTATCA
Found at i:1287707 original size:21 final size:21
Alignment explanation
Indices: 1287689--1287736 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
1287679 ATATGTATTG
1287689 ATACATGCACAAAATGTATCA
1 ATACATGCACAAAATGTATCA
1287710 ATACATGCACAAAATGTATCA
1 ATACATGCACAAAATGTATCA
1287731 ATACAT
1 ATACAT
1287737 TCAATCCTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.48, C:0.19, G:0.08, T:0.25
Consensus pattern (21 bp):
ATACATGCACAAAATGTATCA
Found at i:1288014 original size:23 final size:23
Alignment explanation
Indices: 1287988--1288037 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
1287978 CGTCCATCAA
*
1287988 ATATCTATATGAATGGGT-AAGAT
1 ATATCTAAAT-AATGGGTAAAGAT
*
1288011 ATATCTAAATAATTGGTAAAGAT
1 ATATCTAAATAATGGGTAAAGAT
1288034 ATAT
1 ATAT
1288038 TCAAACAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.44, C:0.04, G:0.16, T:0.36
Consensus pattern (23 bp):
ATATCTAAATAATGGGTAAAGAT
Found at i:1288050 original size:23 final size:23
Alignment explanation
Indices: 1288006--1288053 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1287996 ATGAATGGGT
* *
1288006 AAGATATATCTAAATAATTGGTA
1 AAGATATATCTAAACAAGTGGTA
1288029 AAGATATAT-TCAAACAAGTGGTA
1 AAGATATATCT-AAACAAGTGGTA
1288052 AA
1 AA
1288054 AAGATTTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 21 0.95
ACGTcount: A:0.50, C:0.06, G:0.15, T:0.29
Consensus pattern (23 bp):
AAGATATATCTAAACAAGTGGTA
Found at i:1291366 original size:18 final size:18
Alignment explanation
Indices: 1291332--1291366 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1291322 AATCAATTAA
* *
1291332 ATAACAAATTGATTTTAC
1 ATAACAAATTAAGTTTAC
1291350 ATAACAAATTAAGTTTA
1 ATAACAAATTAAGTTTA
1291367 TTCATTTTGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.09, G:0.06, T:0.37
Consensus pattern (18 bp):
ATAACAAATTAAGTTTAC
Found at i:1294813 original size:2 final size:2
Alignment explanation
Indices: 1294806--1294835 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1294796 TTTTGTTCTG
1294806 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1294836 TATTATGCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1295115 original size:16 final size:16
Alignment explanation
Indices: 1295058--1295123 Score: 50
Period size: 14 Copynumber: 4.2 Consensus size: 16
1295048 ATTAAATTGA
1295058 AATATAATTTAATGAATTT
1 AATA-AATTTAAT--ATTT
* *
1295077 -ATAAAATT-ATTTTT
1 AATAAATTTAATATTT
1295091 AAT-AA-TTAATATTT
1 AATAAATTTAATATTT
*
1295105 AATAAATTTAAAATTT
1 AATAAATTTAATATTT
1295121 AAT
1 AAT
1295124 TTTTAACCCA
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
13 2 0.05
14 13 0.33
15 4 0.10
16 13 0.33
17 4 0.10
18 3 0.08
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (16 bp):
AATAAATTTAATATTT
Found at i:1303659 original size:16 final size:16
Alignment explanation
Indices: 1303638--1303685 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
1303628 ATTTATATAA
1303638 ATTTTAAAATATTAAT
1 ATTTTAAAATATTAAT
* * * *
1303654 ATTTTATATTATAAAA
1 ATTTTAAAATATTAAT
*
1303670 ATTTTAATATATTAAT
1 ATTTTAAAATATTAAT
1303686 TTATTTATAT
Statistics
Matches: 23, Mismatches: 9, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTTTAAAATATTAAT
Found at i:1303672 original size:32 final size:33
Alignment explanation
Indices: 1303630--1303697 Score: 102
Period size: 32 Copynumber: 2.1 Consensus size: 33
1303620 TATTATAAAT
*
1303630 TTATATAAATTTTAAAATATTAATAT-TTTATA
1 TTATAAAAATTTTAAAATATTAATATATTTATA
* *
1303662 TTATAAAAATTTTAATATATTAATTTATTTATA
1 TTATAAAAATTTTAAAATATTAATATATTTATA
1303695 TTA
1 TTA
1303698 CATTTAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 23 0.72
33 9 0.28
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (33 bp):
TTATAAAAATTTTAAAATATTAATATATTTATA
Found at i:1303689 original size:24 final size:23
Alignment explanation
Indices: 1303631--1303689 Score: 59
Period size: 24 Copynumber: 2.6 Consensus size: 23
1303621 ATTATAAATT
*
1303631 TATATAAATTT-TAAAATATTAA
1 TATATTAATTTATAAAATATTAA
* *
1303653 TAT-TTTATATTATAAAAATTTTAA
1 TATATTAAT-TTAT-AAAATATTAA
1303677 TATATTAATTTAT
1 TATATTAATTTAT
1303690 TTATATTACA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
21 3 0.10
22 5 0.17
23 1 0.03
24 16 0.55
25 4 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TATATTAATTTATAAAATATTAA
Found at i:1304330 original size:14 final size:17
Alignment explanation
Indices: 1304291--1304339 Score: 66
Period size: 18 Copynumber: 2.9 Consensus size: 17
1304281 AGTAAGAGTA
1304291 TATTAG-TTATAATTAT
1 TATTAGATTATAATTAT
1304307 TATTAGATTATAATTATT
1 TATTAGATTATAATTA-T
1304325 TAATTA-ATTATAATT
1 T-ATTAGATTATAATT
1304340 TAAAATTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.20
17 9 0.30
18 11 0.37
19 4 0.13
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (17 bp):
TATTAGATTATAATTAT
Found at i:1307632 original size:37 final size:38
Alignment explanation
Indices: 1307581--1307666 Score: 111
Period size: 37 Copynumber: 2.3 Consensus size: 38
1307571 ATTAGAAATC
* * *
1307581 AGTTTCAAATTGTGTCACTGATTGAGAATAGTAGTTTT
1 AGTTTCAAACTGTGTCACCGATTGAGAATAATAGTTTT
* *
1307619 -GTTTCAAACTGTGTCACCGGTTGGGAATAATAGTTTT
1 AGTTTCAAACTGTGTCACCGATTGAGAATAATAGTTTT
*
1307656 AATTTCAAACT
1 AGTTTCAAACT
1307667 ATGCTATCGT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
37 32 0.78
38 9 0.22
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.40
Consensus pattern (38 bp):
AGTTTCAAACTGTGTCACCGATTGAGAATAATAGTTTT
Done.