Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009636.1 Hibiscus syriacus cultivar Beakdansim tig00117040_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 700957
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
File 2 of 4
Found at i:235194 original size:46 final size:41
Alignment explanation
Indices: 235141--235233 Score: 107
Period size: 44 Copynumber: 2.2 Consensus size: 41
235131 TTTAGATTAC
* *
235141 ATATATATGTATATGTTACT-TTTTATTATCTGTTTTATTAATTT
1 ATATATATATATA-CTTACTATTTT-TTATCT-TTTTATTAA-TT
* *
235185 ATATATATATATACTTACTATTTTTTATGTTTTTATTTATT
1 ATATATATATATACTTACTATTTTTTATCTTTTTATTAATT
235226 ATATATAT
1 ATATATAT
235234 TATTTTTTCT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
41 10 0.23
42 8 0.18
43 10 0.23
44 16 0.36
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.61
Consensus pattern (41 bp):
ATATATATATATACTTACTATTTTTTATCTTTTTATTAATT
Found at i:235254 original size:33 final size:33
Alignment explanation
Indices: 235183--235274 Score: 87
Period size: 34 Copynumber: 2.7 Consensus size: 33
235173 TTTTATTAAT
*
235183 TTATATATATATATACTTACTATTTTTTATGTTTTTA
1 TTATAT-TATATATA-TTA-T-TTTTTTATGTTATTA
*
235220 TT-TATTATATATATTATTTTTTCTTTGTTATTA
1 TTATATTATATATATTATTTTTT-TATGTTATTA
* * *
235253 TTATTTTATTTATATAATTTTT
1 TTATATTATATATATTATTTTT
235275 CCTTCTTTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
32 5 0.10
33 11 0.23
34 19 0.40
35 8 0.17
36 3 0.06
37 2 0.04
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.67
Consensus pattern (33 bp):
TTATATTATATATATTATTTTTTTATGTTATTA
Found at i:244623 original size:20 final size:21
Alignment explanation
Indices: 244575--244634 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 21
244565 CAACTCAGTT
*
244575 TCAA-ATTCGCAACGCGAATA
1 TCAAGATTCGCAACGCGATTA
* *
244595 TCCAGATTCGCAACGCGATTG
1 TCAAGATTCGCAACGCGATTA
244616 T-AAGATTCGCAACGCGATT
1 TCAAGATTCGCAACGCGATT
244635 TTGAAAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 20 0.57
21 15 0.43
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (21 bp):
TCAAGATTCGCAACGCGATTA
Found at i:244717 original size:19 final size:19
Alignment explanation
Indices: 244689--244725 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
244679 AAAAACGTGT
*
244689 TGTTGTGATAGTGAAAAAG
1 TGTTGCGATAGTGAAAAAG
244708 TGTTGCGATAGTGAAAAA
1 TGTTGCGATAGTGAAAAA
244726 TTCAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.30, T:0.30
Consensus pattern (19 bp):
TGTTGCGATAGTGAAAAAG
Found at i:245215 original size:21 final size:21
Alignment explanation
Indices: 245156--245342 Score: 170
Period size: 21 Copynumber: 9.2 Consensus size: 21
245146 GCGAACTTCG
* *
245156 AACGTGAACTTGGACTGTCGC
1 AACGCGAACTTGGACTATCGC
* **
245177 AA--CGAATTTGGAAAATCGC
1 AACGCGAACTTGGACTATCGC
*
245196 AACGCGAACTTCGACTATCGC
1 AACGCGAACTTGGACTATCGC
* **
245217 AA--CGAATTTGGAAAATCGC
1 AACGCGAACTTGGACTATCGC
* *
245236 AACGTGAACTTGGACTATCAC
1 AACGCGAACTTGGACTATCGC
*
245257 AACGTGAACTTGGACTATCGC
1 AACGCGAACTTGGACTATCGC
* **
245278 AA--CGAATTTGGAAAATCGC
1 AACGCGAACTTGGACTATCGC
*
245297 AACGCGAACTTCGACTATCGC
1 AACGCGAACTTGGACTATCGC
* *
245318 AACGTGAACTTGGACTATCGT
1 AACGCGAACTTGGACTATCGC
245339 AACG
1 AACG
245343 AATTTGTACT
Statistics
Matches: 130, Mismatches: 30, Indels: 12
0.76 0.17 0.07
Matches are distributed among these distances:
19 44 0.34
21 86 0.66
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.22
Consensus pattern (21 bp):
AACGCGAACTTGGACTATCGC
Found at i:245217 original size:40 final size:40
Alignment explanation
Indices: 245156--245348 Score: 201
Period size: 40 Copynumber: 4.8 Consensus size: 40
245146 GCGAACTTCG
*
245156 AACGTGAACTTGGACTGTCGCAACGAATTTGGAAAATCGC
1 AACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGC
* *
245196 AACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCGC
1 AACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGC
* * **
245236 AACGTGAACTTGGACTATCACAACGTGAACTTGGACTATCGC
1 AACGTGAACTTGGACTATCGCAAC--GAATTTGGAAAATCGC
* ** * * **
245278 AAC--GAATTTGGAAAATCGCAACGCGAACTTCGACTATCGC
1 AACGTGAACTTGGACTATCGCAA--CGAATTTGGAAAATCGC
*
245318 AACGTGAACTTGGACTATCGTAACGAATTTG
1 AACGTGAACTTGGACTATCGCAACGAATTTG
245349 TACTAACGTA
Statistics
Matches: 127, Mismatches: 20, Indels: 12
0.80 0.13 0.08
Matches are distributed among these distances:
40 96 0.76
42 31 0.24
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.23
Consensus pattern (40 bp):
AACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGC
Found at i:245266 original size:61 final size:61
Alignment explanation
Indices: 245195--245348 Score: 254
Period size: 61 Copynumber: 2.5 Consensus size: 61
245185 TGGAAAATCG
* * * *
245195 CAACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCAACGTGAACTTGGACTATCA
1 CAACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCA
*
245256 CAACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCG
1 CAACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCA
*
245317 CAACGTGAACTTGGACTATCGTAACGAATTTG
1 CAACGTGAACTTGGACTATCGCAACGAATTTG
245349 TACTAACGTA
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 87 1.00
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (61 bp):
CAACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCA
Found at i:245382 original size:77 final size:80
Alignment explanation
Indices: 245231--245396 Score: 230
Period size: 77 Copynumber: 2.1 Consensus size: 80
245221 AATTTGGAAA
*
245231 ATCGCAACGTGAACTTGGACTATCACAACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCG
1 ATCGCAACGTGAACTTGGACTATCACAACG-GAACTTGGACTAACGCAAC-AATTTGGAAAATCG
245296 CAACGCGAACTTCGACT
64 CAACGCGAACTTCGACT
** * * *
245313 ATCGCAACGTGAACTTGGACTATCGTAAC-GAATTTGTACTAACG-TA-AATTTGGAAAATCGCA
1 ATCGCAACGTGAACTTGGACTATCACAACGGAACTTGGACTAACGCAACAATTTGGAAAATCGCA
*
245375 ACGCGAACTTGGACT
66 ACGCGAACTTCGACT
245390 ATCGCAA
1 ATCGCAA
245397 AATCGCGTTG
Statistics
Matches: 77, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
77 37 0.48
79 1 0.01
80 12 0.16
82 27 0.35
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.23
Consensus pattern (80 bp):
ATCGCAACGTGAACTTGGACTATCACAACGGAACTTGGACTAACGCAACAATTTGGAAAATCGCA
ACGCGAACTTCGACT
Found at i:255764 original size:18 final size:18
Alignment explanation
Indices: 255737--255788 Score: 81
Period size: 18 Copynumber: 3.0 Consensus size: 18
255727 TTAAAGTAAG
255737 GGGGAGTAATTTCAAAAC
1 GGGGAGTAATTTCAAAAC
*
255755 GGGGAATAATTTCAAAAC
1 GGGGAGTAATTTCAAAAC
255773 --GGAGTAATTTCAAAAC
1 GGGGAGTAATTTCAAAAC
255789 TTGATTTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
16 15 0.47
18 17 0.53
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.23
Consensus pattern (18 bp):
GGGGAGTAATTTCAAAAC
Found at i:256106 original size:22 final size:22
Alignment explanation
Indices: 256078--256133 Score: 112
Period size: 22 Copynumber: 2.5 Consensus size: 22
256068 CTCAGAGGAA
256078 ACCGATTCCCCCCCAAGGGGGT
1 ACCGATTCCCCCCCAAGGGGGT
256100 ACCGATTCCCCCCCAAGGGGGT
1 ACCGATTCCCCCCCAAGGGGGT
256122 ACCGATTCCCCC
1 ACCGATTCCCCC
256134 TGAATGGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.18, C:0.45, G:0.23, T:0.14
Consensus pattern (22 bp):
ACCGATTCCCCCCCAAGGGGGT
Found at i:258084 original size:23 final size:23
Alignment explanation
Indices: 258054--258120 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
258044 ACCTTATATA
*
258054 GCACTTCGATGCATTTCTACGCG
1 GCACTTCGGTGCATTTCTACGCG
* **
258077 GCACTTCGGTGCAATTCTACATG
1 GCACTTCGGTGCATTTCTACGCG
*
258100 GCACTTCGGTGCATTTATACG
1 GCACTTCGGTGCATTTCTACG
258121 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.19, C:0.27, G:0.22, T:0.31
Consensus pattern (23 bp):
GCACTTCGGTGCATTTCTACGCG
Found at i:262244 original size:5 final size:5
Alignment explanation
Indices: 262234--262306 Score: 57
Period size: 5 Copynumber: 15.4 Consensus size: 5
262224 TAGATATAAA
* * * **
262234 AAAAT AAAAT -AAAT TAAAT -AAAT -AAAT -AAAT AAATT CAACC AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
262280 AAAA- AGAAAT AAAAT AAAAT AAAAT AA
1 AAAAT A-AAAT AAAAT AAAAT AAAAT AA
262307 TAAATAAATA
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
4 17 0.30
5 39 0.68
6 1 0.02
ACGTcount: A:0.74, C:0.04, G:0.01, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:262255 original size:4 final size:4
Alignment explanation
Indices: 262229--262322 Score: 61
Period size: 4 Copynumber: 22.2 Consensus size: 4
262219 CATGTTAGAT
*
262229 ATAA AAAA ATAAA ATAA ATTAA ATAA ATAA ATAA ATAA ATTCAA CCA-AA
1 ATAA ATAA AT-AA ATAA A-TAA ATAA ATAA ATAA ATAA A-T-AA --ATAA
*
262278 AT-A A-AA AGAA ATAAA ATAAA ATAA A-ATA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA AT-AA AT-AA ATAA ATA-A ATAA ATAA ATAA ATAA A
262323 GCATAGAAAA
Statistics
Matches: 75, Mismatches: 3, Indels: 24
0.74 0.03 0.24
Matches are distributed among these distances:
3 6 0.08
4 45 0.60
5 21 0.28
6 2 0.03
8 1 0.01
ACGTcount: A:0.74, C:0.03, G:0.01, T:0.21
Consensus pattern (4 bp):
ATAA
Found at i:263094 original size:37 final size:36
Alignment explanation
Indices: 263051--263152 Score: 165
Period size: 34 Copynumber: 2.9 Consensus size: 36
263041 TTAGTAGAAC
263051 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
263088 GT-TATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 -TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
263122 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
263153 TAGGACGAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
33 1 0.02
34 32 0.52
37 27 0.44
38 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:264011 original size:105 final size:104
Alignment explanation
Indices: 263700--264255 Score: 690
Period size: 105 Copynumber: 5.3 Consensus size: 104
263690 CATTGTTCCA
* * ** * *
263700 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAATTGGGAAGTTG-TTGTTGACAAG
* * * * *
263765 CAGCCGTCCCTTCGTTGTGAAGTTAAACTTGTGTTGTCTCG
64 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
263806 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAAC-CTGAA-T--GAAATT-TTGTTGACAAGT
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTG-GCTCTGAATTGGGAAGTTGTTGTTGACAAGC
263866 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
263906 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA-ATTGGGAAGTTGTTGTTGACAAGC
** * * *
263971 AATGGTCTCTTCGTCGTGAAGTTGAACTTGCATTGCCTGG
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
264011 AGTCTAATATACTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-AATTGGGAAGTTGTTGTTGACAAGC
* *
264076 AGCGGTCTCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
264116 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGCAATTGAGAAGTTTTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-AATTGGGAAG-TTGTTGTTGACAAG
* * * *
264181 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
64 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
264222 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
264256 CGCGGATGGC
Statistics
Matches: 397, Mismatches: 41, Indels: 21
0.86 0.09 0.05
Matches are distributed among these distances:
99 1 0.00
100 82 0.21
101 1 0.00
102 7 0.02
104 5 0.01
105 191 0.48
106 84 0.21
107 4 0.01
109 22 0.06
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (104 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTGGGAAGTTGTTGTTGACAAGCA
GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:264982 original size:67 final size:65
Alignment explanation
Indices: 264859--265308 Score: 273
Period size: 65 Copynumber: 6.7 Consensus size: 65
264849 AAGATATCTG
* * * * **
264859 TTGTTTCATGAGAAACGGTCTCAAGGGAAACACAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT-TGTTTTAAGGGAAATAAATTCAAAGA-
264924 TT
64 TT
* *
264926 TGTGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGAT
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAT
264991 T
65 T
* ** * * * **
264992 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGTTTCAAGAGAAAT-TGTCTCAAGAGA
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAAT-TC-A-A-A
*
265056 GACAAAACT
62 G-----ATT
* * * * * * * * * *
265065 TAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATTCAAATATT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
* * * * *
265130 TTGTTTCAAGGGAAACTGTCTCAA--GAGGCAAAATTTATTTCAAGGGAAACTGTCTCAAGAGAG
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA-----T--A-A-AT
*
265193 ACAAA-ATT
57 TCAAAGATT
* * * * * *** *
265201 TTGTTTCAAG-GAAAACTATCTCAAGAGAGACGAAATTTATTTCAAGGGAAATGTTTTCAATG-T
1 TTGTTTCAAGAG-AAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAT
265264 T
65 T
265265 TATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTT
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTT
265309 TTAAAAAAAA
Statistics
Matches: 298, Mismatches: 59, Indels: 54
0.73 0.14 0.13
Matches are distributed among these distances:
63 20 0.07
64 7 0.02
65 102 0.34
66 5 0.02
67 25 0.08
68 34 0.11
70 3 0.01
71 25 0.08
72 6 0.02
73 69 0.23
74 2 0.01
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (65 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
Found at i:265048 original size:36 final size:36
Alignment explanation
Indices: 264991--265251 Score: 245
Period size: 36 Copynumber: 7.4 Consensus size: 36
264981 ATTCAAAGAT
* *
264991 TTTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* *
265027 TTTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * ** * *
265063 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * * * *
265100 TTTGTTTCAAAGAAAACATAT-TC-----A-A-ATAT
1 TTTGTTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAA
265129 TTTGTTTCAAGGGAAACTGTCTCAAGAG-G-CAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
265163 TTTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * *
265199 TTTTGTTTCAAGGAAAACTATCTCAAGAGAGACGAAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
265236 TTTATTTCAAGGGAAA
1 TTTGTTTCAAGGGAAA
265252 TGTTTTCAAT
Statistics
Matches: 182, Mismatches: 30, Indels: 26
0.76 0.13 0.11
Matches are distributed among these distances:
28 2 0.01
29 18 0.10
30 1 0.01
31 1 0.01
34 29 0.16
35 1 0.01
36 66 0.36
37 64 0.35
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:265051 original size:15 final size:16
Alignment explanation
Indices: 265023--265055 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
265013 CAAGATAGAC
*
265023 GAAATTTGTTTCAAGA
1 GAAATTTGTCTCAAGA
265039 GAAA-TTGTCTCAAGA
1 GAAATTTGTCTCAAGA
265054 GA
1 GA
265056 GACAAAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.30
Consensus pattern (16 bp):
GAAATTTGTCTCAAGA
Found at i:265085 original size:37 final size:36
Alignment explanation
Indices: 265003--265114 Score: 118
Period size: 37 Copynumber: 3.1 Consensus size: 36
264993 TGTTTCAAGG
* * * * *
265003 GAAACTGTCTCAAGATAGACGAAATTTGTTTCAAGA
1 GAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAA
*
265039 GAAATTGTCTCAAGAGAGACAAAACTTAGTTCCAAAA
1 GAAACTGTCTCAAGAGAGACAAAA-TTAGTTCCAAAA
* * * *
265076 GAAACTGTCTCAAGGGAGACGAAATTTGTTTC-AAA
1 GAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAA
265111 GAAA
1 GAAA
265115 ACATATTCAA
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
35 7 0.11
36 27 0.42
37 30 0.47
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.24
Consensus pattern (36 bp):
GAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAA
Found at i:265101 original size:138 final size:136
Alignment explanation
Indices: 264940--265307 Score: 452
Period size: 136 Copynumber: 2.7 Consensus size: 136
264930 TTTCAAGAGT
* * * *
264940 AACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAAGATTTTGTTTCAAGGGA
* *
265005 AACTGTCTCAAGATAGACGAAATTTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTAGTT
66 AACTGTCTCAAG--AGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTT
265070 CCAAA-AGA
129 CCAAAGA-A
* * * *
265078 AACTGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAAGATTTTGTTTCAAGGGA
* * * * * *
265143 AACTGTCTCAAGAGGCAAAATTTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTTGTTTC
66 AACTGTCTCAAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCC
*
265208 AAGGAA
131 AAAGAA
* * * * * * *
265214 AACTATCTCAAGAGAGACGAAATTTATTTCAAGGGAAATGTTTTCAATG-TTTATGTTTCAAGAG
1 AACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAAGATTT-TGTTTCAAGGG
265278 AAACTGTCTCAAGGGAGACAAAATTTGTTT
65 AAACTGTCTCAA--GAGACAAAATTTGTTT
265308 TTTAAAAAAA
Statistics
Matches: 196, Mismatches: 30, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
135 3 0.02
136 109 0.56
137 1 0.01
138 83 0.42
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (136 bp):
AACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAAGATTTTGTTTCAAGGGA
AACTGTCTCAAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCC
AAAGAA
Found at i:265201 original size:99 final size:103
Alignment explanation
Indices: 265027--265224 Score: 271
Period size: 99 Copynumber: 2.0 Consensus size: 103
265017 ATAGACGAAA
* *
265027 TTTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGG
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAG
*
265092 AGACGAAA-TTTGTTTCAAAGAAAACATAT-TCAAATAT
66 AGACAAAATTTTGTTTCAAAGAAAAC-TATCTCAAATAT
* * * **
265129 TTTGTTTCAAGGGAAACTGTCTCAAGAG-G-CAAAATTTA-TTTCAAGGGAAACTGTCTCAAGAG
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAG
*
265191 AGACAAAATTTTGTTTCAAGGAAAACTATCTCAA
66 AGACAAAATTTTGTTTCAAAGAAAACTATCTCAA
265225 GAGAGACGAA
Statistics
Matches: 85, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
99 30 0.35
100 28 0.33
101 1 0.01
102 26 0.31
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (103 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAG
AGACAAAATTTTGTTTCAAAGAAAACTATCTCAAATAT
Found at i:265217 original size:37 final size:36
Alignment explanation
Indices: 265133--265251 Score: 179
Period size: 37 Copynumber: 3.3 Consensus size: 36
265123 AAATATTTTG
265133 TTTCAAGGGAAACTGTCTCAAGAG-G-CAAAATTTA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA
*
265167 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTTG
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTA
* * *
265204 TTTCAAGGAAAACTATCTCAAGAGAGACGAAATTTA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA
265240 TTTCAAGGGAAA
1 TTTCAAGGGAAA
265252 TGTTTTCAAT
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
34 24 0.32
35 1 0.01
36 19 0.25
37 32 0.42
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.26
Consensus pattern (36 bp):
TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA
Found at i:266129 original size:22 final size:22
Alignment explanation
Indices: 266103--266157 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
266093 TTGTGTTTGG
266103 TCAAAGGTTTGGCATTTGATAC
1 TCAAAGGTTTGGCATTTGATAC
*
266125 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATAC
266147 TCAAAGGTTTG
1 TCAAAGGTTTG
266158 ATGGGATAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATAC
Found at i:266822 original size:10 final size:9
Alignment explanation
Indices: 266792--266884 Score: 64
Period size: 9 Copynumber: 9.7 Consensus size: 9
266782 TTTGTTCCTC
266792 TTTCTTTTT
1 TTTCTTTTT
266801 TATTCTTATTT
1 T-TTCTT-TTT
*
266812 TTTCATTTT
1 TTTCTTTTT
*
266821 TTTCCTTTT
1 TTTCTTTTT
*
266830 GTTCTTTTT
1 TTTCTTTTT
*
266839 TCTCTTTTT
1 TTTCTTTTT
266848 TCTT-TGTTTT
1 T-TTCT-TTTT
266858 TTT-TTGCTTCT
1 TTTCTT--TT-T
266869 TTTCTTTTT
1 TTTCTTTTT
266878 TCTTCTT
1 T-TTCTT
266885 GATTGGATCT
Statistics
Matches: 68, Mismatches: 7, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
8 1 0.01
9 33 0.49
10 24 0.35
11 8 0.12
12 2 0.03
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.78
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:266846 original size:25 final size:24
Alignment explanation
Indices: 266809--266881 Score: 75
Period size: 23 Copynumber: 3.1 Consensus size: 24
266799 TTTATTCTTA
266809 TTTTTTCAT-TTTTTTCCTTTTGTTC
1 TTTTTTC-TCTTTTTT-CTTTTGTTC
266834 TTTTTTCTCTTTTTTC-TTTGTT-
1 TTTTTTCTCTTTTTTCTTTTGTTC
266856 TTTTTT-TGCTTCTTTTCTTTT-TTC
1 TTTTTTCT-CTT-TTTTCTTTTGTTC
266880 TT
1 TT
266882 CTTGATTGGA
Statistics
Matches: 43, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
21 1 0.02
22 9 0.21
23 13 0.30
24 7 0.16
25 13 0.30
ACGTcount: A:0.01, C:0.15, G:0.04, T:0.79
Consensus pattern (24 bp):
TTTTTTCTCTTTTTTCTTTTGTTC
Found at i:269902 original size:12 final size:12
Alignment explanation
Indices: 269884--269971 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 12
269874 GTTAGATATA
269884 AAAAAAATGAAAT
1 AAAAAAAT-AAAT
269897 AAAAAAATAAAT
1 AAAAAAATAAAT
* **
269909 AAATTCAACCAAA-
1 AAA--AAAATAAAT
* *
269922 ATAAAAAGAAAT
1 AAAAAAATAAAT
269934 AAAATAAAATAAAAT
1 -AAA-AAAAT-AAAT
*
269949 AAAATAATAAAT
1 AAAAAAATAAAT
*
269961 AAATAAATAAA
1 AAAAAAATAAA
269972 GCATAGAAAA
Statistics
Matches: 57, Mismatches: 12, Indels: 13
0.70 0.15 0.16
Matches are distributed among these distances:
11 5 0.09
12 20 0.35
13 16 0.28
14 12 0.21
15 4 0.07
ACGTcount: A:0.76, C:0.03, G:0.02, T:0.18
Consensus pattern (12 bp):
AAAAAAATAAAT
Found at i:269937 original size:15 final size:14
Alignment explanation
Indices: 269919--269971 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 14
269909 AAATTCAACC
269919 AAAATAAAAAGAAAT
1 AAAATAAAAA-AAAT
269934 AAAATAAAATAAAAT
1 AAAATAAAA-AAAAT
269949 AAAATAATAAATAAAT
1 AAAATAA-AAA-AAAT
269965 -AAATAAA
1 AAAATAAA
269972 GCATAGAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
14 1 0.03
15 27 0.77
16 7 0.20
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (14 bp):
AAAATAAAAAAAAT
Found at i:269938 original size:5 final size:5
Alignment explanation
Indices: 269881--269955 Score: 61
Period size: 5 Copynumber: 15.8 Consensus size: 5
269871 CATGTTAGAT
* * * **
269881 ATAAA A-AAA ATGAA AT-AA A-AAA AT-AA ATAAA TTCAA CCAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
269927 A-AGAA ATAAA ATAAA ATAAA ATAAA ATAA
1 ATA-AA ATAAA ATAAA ATAAA ATAAA ATAA
269956 TAAATAAATA
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
4 15 0.27
5 40 0.71
6 1 0.02
ACGTcount: A:0.76, C:0.04, G:0.03, T:0.17
Consensus pattern (5 bp):
ATAAA
Found at i:270082 original size:74 final size:73
Alignment explanation
Indices: 269932--270103 Score: 172
Period size: 74 Copynumber: 2.3 Consensus size: 73
269922 ATAAAAAGAA
** * * *
269932 ATAAAATAAAATAAAATAAAATAATAAATAAATAAATAAAGCATAGAAAAATGATAGTAAATAAT
1 ATAAAATAAAA-AAGGTAATATAATAAATAAATAAATAAAGCATAAAAAAATGATAGCAAATAAT
269997 AGTATAAAT
65 AGTATAAAT
*
270006 ATAAAATAAAAAAGGTAATATATATAAATAAATAAAATACA-CATAAAGAAAATGA-AGC-AATA
1 ATAAAATAAAAAAGGTAATATA-ATAAATAAAT-AAATAAAGCATAAA-AAAATGATAGCAAAT-
*
270068 AATA-TGATATAT
62 AATAGT-ATAAAT
*
270080 ATAATAATGATAAAAGGTAATATA
1 ATAA-AAT-AAAAAAGGTAATATA
270104 CGTAAATAGA
Statistics
Matches: 83, Mismatches: 8, Indels: 12
0.81 0.08 0.12
Matches are distributed among these distances:
73 12 0.14
74 41 0.49
75 16 0.19
76 14 0.17
ACGTcount: A:0.65, C:0.02, G:0.08, T:0.25
Consensus pattern (73 bp):
ATAAAATAAAAAAGGTAATATAATAAATAAATAAATAAAGCATAAAAAAATGATAGCAAATAATA
GTATAAAT
Found at i:270718 original size:37 final size:35
Alignment explanation
Indices: 270668--270837 Score: 202
Period size: 34 Copynumber: 4.8 Consensus size: 35
270658 GTGCTTGTGG
* * * * *
270668 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAG-A-AATTCT
270705 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATGT-T
1 ATCCTATTTTTAGGAGTTTGAATCCTAG--AAAT-TCT
*
270742 ATCCTATTTTTAAGAGTTTGAATCCTA-AAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGAAATTCT
*
270776 ATCATATTTTTAGGAGTTTGAATCCTA-AAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGAAATTCT
*
270810 ATCATATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
270838 TATGACGAAA
Statistics
Matches: 120, Mismatches: 9, Indels: 10
0.86 0.06 0.07
Matches are distributed among these distances:
33 1 0.01
34 64 0.53
37 53 0.44
38 2 0.02
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (35 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGAAATTCT
Found at i:271066 original size:21 final size:21
Alignment explanation
Indices: 271040--271079 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
271030 AAAAAATATT
*
271040 TAAAAACAATAATGTTTTAGA
1 TAAAAACAATAATATTTTAGA
*
271061 TAAAAATAATAATATTTTA
1 TAAAAACAATAATATTTTA
271080 AATATTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.38
Consensus pattern (21 bp):
TAAAAACAATAATATTTTAGA
Found at i:279475 original size:16 final size:16
Alignment explanation
Indices: 279454--279493 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 16
279444 ATATTTACTA
279454 AATTTATATATATTTT
1 AATTTATATATATTTT
279470 AATTTA-A-ATATTTT
1 AATTTATATATATTTT
*
279484 -ATTTTTATAT
1 AATTTATATAT
279494 GAATCAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
13 4 0.19
14 8 0.38
15 3 0.14
16 6 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
AATTTATATATATTTT
Found at i:280221 original size:30 final size:30
Alignment explanation
Indices: 280185--280255 Score: 142
Period size: 30 Copynumber: 2.4 Consensus size: 30
280175 ACCCTCATCC
280185 ACTCACCTATATATATATCTGCCCCCACTA
1 ACTCACCTATATATATATCTGCCCCCACTA
280215 ACTCACCTATATATATATCTGCCCCCACTA
1 ACTCACCTATATATATATCTGCCCCCACTA
280245 ACTCACCTATA
1 ACTCACCTATA
280256 CAAATAACTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.31, C:0.37, G:0.03, T:0.30
Consensus pattern (30 bp):
ACTCACCTATATATATATCTGCCCCCACTA
Found at i:282580 original size:26 final size:26
Alignment explanation
Indices: 282551--282600 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
282541 AAAAATTAAC
*
282551 TCAAGTTCAAGT-TATAAAAAAATTCG
1 TCAAGTTCAA-TAAATAAAAAAATTCG
*
282577 TCAATTTCAATAAATAAAAAAATT
1 TCAAGTTCAATAAATAAAAAAATT
282601 TTAACTCATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 1 0.05
26 20 0.95
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.32
Consensus pattern (26 bp):
TCAAGTTCAATAAATAAAAAAATTCG
Found at i:287199 original size:19 final size:19
Alignment explanation
Indices: 287175--287212 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
287165 GCAGATGCAT
287175 AGATCTAATAAAGAAGCAA
1 AGATCTAATAAAGAAGCAA
287194 AGATCTAATAAAGAAGCAA
1 AGATCTAATAAAGAAGCAA
287213 CATTAACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.58, C:0.11, G:0.16, T:0.16
Consensus pattern (19 bp):
AGATCTAATAAAGAAGCAA
Found at i:305372 original size:225 final size:218
Alignment explanation
Indices: 304843--305617 Score: 833
Period size: 209 Copynumber: 3.6 Consensus size: 218
304833 TGCGATGAAC
* * * *
304843 GTGACCTTCAAATCTTCAATCTGACACTCTCCCAATTGAGTTATTCCCGCTTGTTTTCTTAATGA
1 GTGACCTTCAAATCTTCAATCTGACGCTCTCCCAATTGAGCTATCCCCGCTAGTTTTCTTAATGA
** * *
304908 ACATTTCAATTTAGATATTCAGTCTGAACTCCATAGATCTTATGCTCTTCA-AAT-AG----T--
66 ACATTTCAATTTAGACCTTCAGTCTGAACTCCATAGATCTTGTGCTCTTCACACTAAGCTTATCG
* ** * *
304965 A-ATTTTTTTATTACATTTAAAATAACTAATGAACCAA-ATAATAATAATGCAATTCAATTAAAA
131 ACATATACTAATTATATTTAAAATAACTAATG-A-CAACATAATAAT-AT-CAATTCAATTAAAA
* * *
305028 TTAGATGCGACGAATGTGAATT-GAACAC
192 TTAGATGCG-TGAATGTG-GTTCGAACAA
* * * * *
305056 GTGACCTTCAAATCTTCAATCTGACGCTCTACCAGTTGAGTTATTCCCGCTTGTTTTCTTAATGA
1 GTGACCTTCAAATCTTCAATCTGACGCTCTCCCAATTGAGCTATCCCCGCTAGTTTTCTTAATGA
* *
305121 ACATTTTAATTTAGACCATCAGTCTGAACTCCATAGATC-TGTGCTCTTCGA-ACTAAGCTTATC
66 ACATTTCAATTTAGACCTTCAGTCTGAACTCCATAGATCTTGTGCTCTTC-ACACTAAGCTTATC
*
305184 GACAGTATAGTAATTATATTTAAAATAACTAATGATTCAAACCATAATAATACTCCAATTCAATT
130 GACA-TATACTAATTATATTTAAAATAACTAATGA--C-AA-CATAATAATA-T-CAATTCAATT
* *
305249 AAAACTAGATGTTGTGAATGTGGTTCGAACAA
188 AAAATTAGATG-CGTGAATGTGGTTCGAACAA
* * * * *
305281 GTAACCTTCAGATCTTTAGTCTGATGCTCTCCCAATTGAGCTATCCCCGCTAGTTTTCTTAATGA
1 GTGACCTTCAAATCTTCAATCTGACGCTCTCCCAATTGAGCTATCCCCGCTAGTTTTCTTAATGA
* *
305346 ACATTTCAATTTAGACCTTTAGTCTGAACTCCATAGATCTTGTGCTTTTCACACTAAGCTTATCG
66 ACATTTCAATTTAGACCTTCAGTCTGAACTCCATAGATCTTGTGCTCTTCACACTAAGCTTATCG
305411 ACAATATACTAATTATATTTAAAATAACTAATG---AC-T--TAA-ATC-A-T-AA-TAAAATTA
131 AC-ATATACTAATTATATTTAAAATAACTAATGACAACATAATAATATCAATTCAATTAAAATTA
* *** * *
305465 GATGAGGTGAGCATGGATCGAACAT
195 GATG-CGTGAATGTGGTTCGAACAA
* * * *
305490 GTGACCTTCAGATCTTCAGTCTGACGCTCTCCCAACTGAACTATCCCCGCTAGTTTTCTTAATGA
1 GTGACCTTCAAATCTTCAATCTGACGCTCTCCCAATTGAGCTATCCCCGCTAGTTTTCTTAATGA
*
305555 ACATTTCAATTTAGACCTTCAGTCTGAACTCCATAGATCTTGTGCTCTTCAGACTAAGCTTAT
66 ACATTTCAATTTAGACCTTCAGTCTGAACTCCATAGATCTTGTGCTCTTCACACTAAGCTTAT
305618 GTGGATCAAA
Statistics
Matches: 490, Mismatches: 52, Indels: 44
0.84 0.09 0.08
Matches are distributed among these distances:
209 145 0.30
210 2 0.00
211 1 0.00
212 10 0.02
213 101 0.21
214 3 0.01
215 1 0.00
216 3 0.01
218 2 0.00
219 1 0.00
220 2 0.00
221 2 0.00
222 25 0.05
223 2 0.00
224 3 0.01
225 133 0.27
226 53 0.11
227 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (218 bp):
GTGACCTTCAAATCTTCAATCTGACGCTCTCCCAATTGAGCTATCCCCGCTAGTTTTCTTAATGA
ACATTTCAATTTAGACCTTCAGTCTGAACTCCATAGATCTTGTGCTCTTCACACTAAGCTTATCG
ACATATACTAATTATATTTAAAATAACTAATGACAACATAATAATATCAATTCAATTAAAATTAG
ATGCGTGAATGTGGTTCGAACAA
Found at i:305736 original size:141 final size:141
Alignment explanation
Indices: 305478--305758 Score: 386
Period size: 141 Copynumber: 2.0 Consensus size: 141
305468 GAGGTGAGCA
* * *
305478 TGGATCGAACATGTGACCTTCAGATCTTCAGTCTGACGCTCTCCCAACTGAACTATCCCCGCTAG
1 TGGATCAAACATGTGACCTTCAAATCTTAAGTCTGACGCTCTCCCAACTGAACTATCCCCGCTAG
* * *
305543 TTTTCTTAATGAACATTTCAATTTAGACCTTCAGTCTGAACTCCATAGATCTTGTGCTCTTCAGA
66 TTTTCTTAATGAACATTTCAATTTAGACATTCAGTCTGAACTCCATAGATCTTGTGATCTTCAAA
305608 CTAAGCTTATG
131 CTAAGCTTATG
* * * *
305619 TGGATCAAACTTGTGACCTTCAAATCTTAAGTCTGATGCTCTCCCAACAT-AGCTATCCCCGCTT
1 TGGATCAAACATGTGACCTTCAAATCTTAAGTCTGACGCTCTCCCAAC-TGAACTATCCCCGCTA
* * * * * *
305683 GTTTTCTTAATGGACATTTCAATTTAGATATTCA-TATTGAACTCCATATATCTTTTGATCTTTA
65 GTTTTCTTAATGAACATTTCAATTTAGACATTCAGT-CTGAACTCCATAGATCTTGTGATCTTCA
305747 AACTAAGCTTAT
129 AACTAAGCTTAT
305759 CAAATTATAA
Statistics
Matches: 122, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
140 1 0.01
141 120 0.98
142 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (141 bp):
TGGATCAAACATGTGACCTTCAAATCTTAAGTCTGACGCTCTCCCAACTGAACTATCCCCGCTAG
TTTTCTTAATGAACATTTCAATTTAGACATTCAGTCTGAACTCCATAGATCTTGTGATCTTCAAA
CTAAGCTTATG
Found at i:308698 original size:13 final size:13
Alignment explanation
Indices: 308680--308715 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
308670 AAGTTGTTCG
308680 ACGAAACCCCTCA
1 ACGAAACCCCTCA
308693 ACGAAACCCCTCA
1 ACGAAACCCCTCA
308706 ACGAAACCCC
1 ACGAAACCCC
308716 GTTTCTTGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.39, C:0.47, G:0.08, T:0.06
Consensus pattern (13 bp):
ACGAAACCCCTCA
Found at i:310460 original size:3 final size:3
Alignment explanation
Indices: 310452--310507 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
310442 AACAAAAGGA
310452 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
310500 AAG AAG AA
1 AAG AAG AA
310508 ATGAATCACT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:314405 original size:226 final size:222
Alignment explanation
Indices: 313934--314732 Score: 907
Period size: 226 Copynumber: 3.6 Consensus size: 222
313924 TGTGCTATGA
* * * * *
313934 ACGTGACCTTCAAATCTTCAATCTGACACTCTCCCAATTAAGTTATTCCCGCTTGTTTTCTTAAT
1 ACGTGACCTTCAGATCTTCAATCTGACGCTCTCCCAATTGAGTTATCCCCGCTAGTTTTCTTAAT
* * *
313999 GAACATTTCAATTTAGATCTTCAGTCTGAACTCCATAGATCTTATGCTC-TTCAAACTAAGCTTA
66 GAACATTTCAATTTAGACCTTCAGTCTGAACTCCATAGATCTTGTGCTCTTTCACACTAAGCTTA
* * * *
314063 TCAATAATATAGTAATTTTTTTATTACATTTAAAATAACTAATGAATCAAATTATAATAATAATG
131 TCGACAATATAGTAA------TA--ATATTTAAAATAACTAATG-ATCAAA-CATAATAAT-AT-
* *
314128 CAATTCAATTAAAATTAGATGCGACGAACGTGAATT-GAAC
184 CAATTCAATTAAAATTAGATGCG-TGAACGTG-GTTCGAAC
* *
314168 ACGTGACCTTCA-ATTCTTCAATCTGACGCTCTCCCAATTGAGTTATTCCCGCTTGTTTTCTTAA
1 ACGTGACCTTCAGA-TCTTCAATCTGACGCTCTCCCAATTGAGTTATCCCCGCTAGTTTTCTTAA
* * *
314232 TGAACATTTTAATTTTGACCTTCAGTCTGAACTCCATAGATCTTGTGCTCTTTGA-ACTAAGCTT
65 TGAACATTTCAATTTAGACCTTCAGTCTGAACTCCATAGATCTTGTGCTCTTTCACACTAAGCTT
314296 ATCGACAATATAGTAATAATATTTAAAATAACTAATGATTCAAACCATAATAATACTCCAATTCA
130 ATCGACAATATAGTAATAATATTTAAAATAACTAATGA-TCAAA-CATAATAATA-T-CAATTCA
* *
314361 ATTAAAACTAGATGTTGTGAACGTGGTTCGAAC
191 ATTAAAATTAGATG-CGTGAACGTGGTTCGAAC
* * * * *
314394 ACGTAACCTTCAGATCTTCAGTCTGATGCTCTCCAAATTGAGTTATCCCCACTAGTTTTCTTAAT
1 ACGTGACCTTCAGATCTTCAATCTGACGCTCTCCCAATTGAGTTATCCCCGCTAGTTTTCTTAAT
* * * *
314459 GAACATTTCAATTTAAACCTTTAGTCTAAACTCCATAGATCTTGTGCT-TTTCACAGTAAGCTTA
66 GAACATTTCAATTTAGACCTTCAGTCTGAACTCCATAGATCTTGTGCTCTTTCACACTAAGCTTA
*
314523 TCGACAATATAGTAATTATATTTAAAATAACTAATG-----AC-T--TAA-ATC-A-T-AA-TAA
131 TCGACAATATAGTAATAATATTTAAAATAACTAATGATCAAACATAATAATATCAATTCAATTAA
* *
314575 AATTAGATGCGGTGAACATGGATCGAAC
196 AATTAGATGC-GTGAACGTGGTTCGAAC
* * * * *
314603 ACGTGACCTTCAGATCTTCAGTCTGACGTTCTCACAACTGAGCTATCCCCGCTAGTTTTCTTAAT
1 ACGTGACCTTCAGATCTTCAATCTGACGCTCTCCCAATTGAGTTATCCCCGCTAGTTTTCTTAAT
* * *
314668 GAACATTTCAATTTTGACCTTCAGTCTGAACTCCATATATCTTGTGCTC-TTCAGACTAAGCTTA
66 GAACATTTCAATTTAGACCTTCAGTCTGAACTCCATAGATCTTGTGCTCTTTCACACTAAGCTTA
314732 T
131 T
314733 GTGGATCAAA
Statistics
Matches: 504, Mismatches: 51, Indels: 45
0.84 0.09 0.08
Matches are distributed among these distances:
209 140 0.28
210 2 0.00
211 1 0.00
212 1 0.00
213 1 0.00
214 1 0.00
215 1 0.00
216 3 0.01
218 1 0.00
219 1 0.00
220 1 0.00
225 8 0.02
226 206 0.41
227 2 0.00
228 2 0.00
233 1 0.00
234 129 0.26
235 3 0.01
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (222 bp):
ACGTGACCTTCAGATCTTCAATCTGACGCTCTCCCAATTGAGTTATCCCCGCTAGTTTTCTTAAT
GAACATTTCAATTTAGACCTTCAGTCTGAACTCCATAGATCTTGTGCTCTTTCACACTAAGCTTA
TCGACAATATAGTAATAATATTTAAAATAACTAATGATCAAACATAATAATATCAATTCAATTAA
AATTAGATGCGTGAACGTGGTTCGAAC
Found at i:314897 original size:141 final size:139
Alignment explanation
Indices: 314608--314876 Score: 328
Period size: 141 Copynumber: 1.9 Consensus size: 139
314598 CGAACACGTG
* * * *
314608 ACCTTCAGATCTTCAGTCTGACGTTCTCACAACTGAGCTATCCCCGCTAGTTTTCTTAATGAACA
1 ACCTTCAAATCTTCAGTCTGACGCTCTCACAACTAAGCTATCCCCACTAGTTTTCTTAATGAACA
* * * ***
314673 TTTCAATTTTGACCTTCAGTCTGAACTCCATATATCTTGTGCTCTTCAGACTAAGCTTATGTGGA
66 TTTCAATTTTGA-CTTCAGACTGAACTCCATATATCTTGTGATCTTCAAACTAAGCTTATGCAAA
* *
314738 TCAAACATGT
130 TCAAAAATCT
* * *
314748 GACCTTCAAATCTTCAGTCTGATGCTCTCCCAACTAAGCTATCCCCACTTGTTTTCTTAATGAAC
1 -ACCTTCAAATCTTCAGTCTGACGCTCTCACAACTAAGCTATCCCCACTAGTTTTCTTAATGAAC
* * *
314813 ATTTCCATTTAT-A-TTCAGACTGAACTCCATATATTTTGTGATCTTTAAACTAAGCTTAT-CAA
65 ATTTCAATTT-TGACTTCAGACTGAACTCCATATATCTTGTGATCTTCAAACTAAGCTTATGCAA
314875 AT
129 AT
314877 TATAATAATA
Statistics
Matches: 111, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
138 2 0.02
139 41 0.37
141 67 0.60
142 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.37
Consensus pattern (139 bp):
ACCTTCAAATCTTCAGTCTGACGCTCTCACAACTAAGCTATCCCCACTAGTTTTCTTAATGAACA
TTTCAATTTTGACTTCAGACTGAACTCCATATATCTTGTGATCTTCAAACTAAGCTTATGCAAAT
CAAAAATCT
Found at i:314909 original size:13 final size:13
Alignment explanation
Indices: 314891--314929 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
314881 ATAATACTCC
314891 AATTCAATTTTAA
1 AATTCAATTTTAA
314904 AATTCAATTTTAA
1 AATTCAATTTTAA
314917 AATTCAATTTTAA
1 AATTCAATTTTAA
314930 TTAAATGCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
AATTCAATTTTAA
Found at i:316151 original size:141 final size:141
Alignment explanation
Indices: 315925--316205 Score: 411
Period size: 141 Copynumber: 2.0 Consensus size: 141
315915 GCGGTGAACA
* * *
315925 TGGATCGAACACGTGACCTTCAGATCTTCAATCTGACGCTCTCCCAACTAAGCTATTCCCGCTAG
1 TGGATCAAACACGTGACCTTCAAATCTTCAATCTGACGCTCTCCCAACTAAGCTATCCCCGCTAG
* ** * *
315990 TTTTCTTAATGAACATTTCAATTTAGACCTTCAGTCTGAACTCCATAGATCTTGTGCTCTTCAGA
66 TTTTCTTAATGAACATTTCAATTTAGACATTCAAACTGAACTCCATAGATCTTGTGATCTTCAAA
316055 CTAAGCTTATG
131 CTAAGCTTATG
* * * *
316066 TGGATCAAACATGTGACCTTCAAATCTT-AAGTCTGATGCTCTCCCAACTGAGCTATCCCCGCTT
1 TGGATCAAACACGTGACCTTCAAATCTTCAA-TCTGACGCTCTCCCAACTAAGCTATCCCCGCTA
* * *
316130 GTTTTCTTAATGAACATTTCAATTTAGATATTCAAACTGAACTCCATATATCTTGTGATCTTTAA
65 GTTTTCTTAATGAACATTTCAATTTAGACATTCAAACTGAACTCCATAGATCTTGTGATCTTCAA
316195 ACTAAGCTTAT
130 ACTAAGCTTAT
316206 CAAATTATAA
Statistics
Matches: 124, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
140 2 0.02
141 122 0.98
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (141 bp):
TGGATCAAACACGTGACCTTCAAATCTTCAATCTGACGCTCTCCCAACTAAGCTATCCCCGCTAG
TTTTCTTAATGAACATTTCAATTTAGACATTCAAACTGAACTCCATAGATCTTGTGATCTTCAAA
CTAAGCTTATG
Found at i:317833 original size:3 final size:3
Alignment explanation
Indices: 317827--317878 Score: 70
Period size: 3 Copynumber: 17.7 Consensus size: 3
317817 TTTTAATATA
** *
317827 TAT TAT TAT TAT TAT CGT TA- TAT TAT TAT TAT TAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
317874 TAT TA
1 TAT TA
317879 ATTTACAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:323831 original size:11 final size:11
Alignment explanation
Indices: 323803--323840 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
323793 AAGAGCAAAG
323803 AGAAAAATCAA
1 AGAAAAATCAA
323814 AGCAAAAATCAA
1 AG-AAAAATCAA
*
323826 AGAAAAAGCAA
1 AGAAAAATCAA
323837 AGAA
1 AGAA
323841 CAAAAAGAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.71, C:0.11, G:0.13, T:0.05
Consensus pattern (11 bp):
AGAAAAATCAA
Found at i:325035 original size:18 final size:18
Alignment explanation
Indices: 325012--325047 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
325002 TCGAGAAAAG
*
325012 TATACACATACATACATA
1 TATACACACACATACATA
*
325030 TATACATACACATACATA
1 TATACACACACATACATA
325048 CATGATACAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.22, G:0.00, T:0.28
Consensus pattern (18 bp):
TATACACACACATACATA
Found at i:325041 original size:22 final size:21
Alignment explanation
Indices: 325013--325058 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 21
325003 CGAGAAAAGT
*
325013 ATACACATACATACATATATAC
1 ATACACATACATACAT-GATAC
325035 ATACACATACATACATGATAC
1 ATACACATACATACATGATAC
325056 ATA
1 ATA
325059 AAATTTGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.50, C:0.22, G:0.02, T:0.26
Consensus pattern (21 bp):
ATACACATACATACATGATAC
Found at i:325702 original size:105 final size:102
Alignment explanation
Indices: 325515--325753 Score: 286
Period size: 105 Copynumber: 2.3 Consensus size: 102
325505 TGAGGATTTT
** * *
325515 AAAACAAATTGCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCACT
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTAGAATTTGATTCACT
*
325580 AAAAACAAAATTAATCTCACCTT-AGATTGTTGTTTCTTTC-
66 AAAAACAAAATTAATCTCA-CTTGAGATCG-T-TTTC--TCA
* * *
325620 AAAACAAATTTTGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTAGAATTTGTTTCAC-
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTAGAATTTGATTCACT
* * *
325684 ATTAAACAAAGTTGATCTCACTTGAGATCGTTTTCTCA
66 A-AAAACAAAATTAATCTCACTTGAGATCGTTTTCTCA
* *
325722 AAAACAAACTTTGTCTCGCTTGAGACAATTTC
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTC
325754 TCTAAAAACA
Statistics
Matches: 117, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
101 2 0.02
102 29 0.25
103 4 0.03
104 5 0.04
105 77 0.66
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (102 bp):
AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTAGAATTTGATTCACT
AAAAACAAAATTAATCTCACTTGAGATCGTTTTCTCA
Found at i:325744 original size:36 final size:36
Alignment explanation
Indices: 325699--325783 Score: 109
Period size: 36 Copynumber: 2.4 Consensus size: 36
325689 ACAAAGTTGA
**
325699 TCTCACTTGAGATCGTTTTCTC-AAAAACAAACTTTG
1 TCTCACTTGAGA-CAATTTCTCTAAAAACAAACTTTG
* *
325735 TCTCGCTTGAGACAATTTCTCTAAAAACAAATTTTG
1 TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
*
325771 TCTCATTTGAGAC
1 TCTCACTTGAGAC
325784 TATATCTTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
35 7 0.17
36 35 0.83
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (36 bp):
TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
Found at i:326107 original size:27 final size:28
Alignment explanation
Indices: 326068--326226 Score: 198
Period size: 29 Copynumber: 5.6 Consensus size: 28
326058 TTCTTTTGAG
326068 GAAAAAAATCTTTGAGTTTGTTCCTCTT
1 GAAAAAAATCTTTGAGTTTGTTCCTCTT
326096 G-AAAAAATCTTTGAGTTTGTTCCTCTT
1 GAAAAAAATCTTTGAGTTTGTTCCTCTT
*
326123 GAAAAAAATCTTTGAGTTTGTTCCTTTT
1 GAAAAAAATCTTTGAGTTTGTTCCTCTT
* *
326151 GAATAAAAATCTTGGAGTTTGTTCCTTTT
1 GAA-AAAAATCTTTGAGTTTGTTCCTCTT
* * *
326180 GAATAAAATTTTTTGAG-TTGTTTCGT-TT
1 GAA-AAAAATCTTTGAGTTTG-TTCCTCTT
326208 GAAACAAAAATCTTTGAGT
1 G-AA-AAAAATCTTTGAGT
326227 CTATTTATTT
Statistics
Matches: 117, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
27 27 0.23
28 35 0.30
29 55 0.47
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.44
Consensus pattern (28 bp):
GAAAAAAATCTTTGAGTTTGTTCCTCTT
Found at i:326169 original size:57 final size:56
Alignment explanation
Indices: 326068--326226 Score: 205
Period size: 57 Copynumber: 2.8 Consensus size: 56
326058 TTCTTTTGAG
*
326068 GAAAAAAATCTTTGAGTTTGTTCCTCTTG-AAAAAATCTTTGAGTTTGTTCCTCTT
1 GAAAAAAATCTTTGAGTTTGTTCCTTTTGAAAAAAATCTTTGAGTTTGTTCCTCTT
* *
326123 GAAAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAATCTTGGAGTTTGTTCCTTTT
1 GAAAAAAATCTTTGAGTTTGTTCCTTTTGAA-AAAAATCTTTGAGTTTGTTCCTCTT
* * * *
326180 GAATAAAATTTTTTGAG-TTGTTTCGTTTGAAACAAAAATCTTTGAGT
1 GAA-AAAAATCTTTGAGTTTGTTCCTTTTG-AA-AAAAATCTTTGAGT
326227 CTATTTATTT
Statistics
Matches: 91, Mismatches: 9, Indels: 5
0.87 0.09 0.05
Matches are distributed among these distances:
55 28 0.31
56 1 0.01
57 36 0.40
58 26 0.29
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.44
Consensus pattern (56 bp):
GAAAAAAATCTTTGAGTTTGTTCCTTTTGAAAAAAATCTTTGAGTTTGTTCCTCTT
Found at i:326366 original size:30 final size:30
Alignment explanation
Indices: 326332--326462 Score: 102
Period size: 30 Copynumber: 4.1 Consensus size: 30
326322 TGTAAAAAAA
* *
326332 AAAAATCTTTGAGATT-GTTTCTTTTGTAAC
1 AAAAATCTTTGAG-TTGGTTTCTTTGGAAAC
326362 AAAAATCTTTGAGTTGGTTTCTTTGGAAAC
1 AAAAATCTTTGAGTTGGTTTCTTTGGAAAC
* * * ** *
326392 AAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAAAC
1 AAAA------ATCT-TTGAGTTGGTTTCTTTGGAAAC
*
326429 AAAAATCTTTGAGTTTGTTTCTTTGGAAAC
1 AAAAATCTTTGAGTTGGTTTCTTTGGAAAC
326459 AAAA
1 AAAA
326463 TTTTGTCTCT
Statistics
Matches: 79, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
29 2 0.03
30 50 0.63
31 3 0.04
36 3 0.04
37 21 0.27
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.43
Consensus pattern (30 bp):
AAAAATCTTTGAGTTGGTTTCTTTGGAAAC
Found at i:326429 original size:37 final size:37
Alignment explanation
Indices: 326379--326505 Score: 126
Period size: 37 Copynumber: 3.6 Consensus size: 37
326369 TTTGAGTTGG
326379 TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
1 TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
* * * * **
326416 TTTCTTTTGAAACAAAA------ATCT-TTGAGTTTG
1 TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
326446 TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
1 TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
326483 TTTCTTTTGGAAA-AAAATCTTTG
1 TTTC-TTTGGAAACAAAAT-TTTG
326506 AATCTGTTTC
Statistics
Matches: 69, Mismatches: 12, Indels: 17
0.70 0.12 0.17
Matches are distributed among these distances:
30 21 0.30
31 3 0.04
36 3 0.04
37 30 0.43
38 12 0.17
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (37 bp):
TTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
Found at i:326457 original size:67 final size:67
Alignment explanation
Indices: 326349--326516 Score: 284
Period size: 67 Copynumber: 2.5 Consensus size: 67
326339 TTTGAGATTG
* *
326349 TTTCTTTTGTAACAAAAATCTTTGAGTTGGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
326414 AA
66 AA
326416 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
326481 AA
66 AA
* * *
326483 TTTCTTTTGGAA-AAAAATCTTTGAATCTGTTTCT
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCT
326517 CTTAAAATGA
Statistics
Matches: 96, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
66 20 0.21
67 76 0.79
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (67 bp):
TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
AA
Found at i:326552 original size:65 final size:65
Alignment explanation
Indices: 326349--326577 Score: 241
Period size: 67 Copynumber: 3.5 Consensus size: 65
326339 TTTGAGATTG
* *
326349 TTTCTTTTGTAACAAAAATCTTTGAGT-TGGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGA
1 TTTCTTTTGGAA-AAAAATCTTTGAATAT-GTTTCTTT-GAAACAAAATTTTGTCTCTCTTAAGA
326413 TAA
63 TAA
* * *
326416 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTGGAA-AAAAATCTTTGAATATGTTTCTTT-GAAACAAAATTTTGTCTCTCTTAAGAT
326481 AA
64 AA
* * * * *
326483 TTTCTTTTGGAAAAAAATCTTTGAATCTGTTTCTCTT-AAA-ATGAATTTTGTATCTCTTGAGAC
1 TTTCTTTTGGAAAAAAATCTTTGAATATGTTTCT-TTGAAACA-AAATTTTGTCTCTCTTAAGAT
*
326546 AG
64 AA
* **
326548 TTTCTCTT-GAAGTAAATCTTTGAATATGTT
1 TTTCTTTTGGAAAAAAATCTTTGAATATGTT
326578 CATTTTGAAA
Statistics
Matches: 146, Mismatches: 13, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
64 20 0.14
65 28 0.19
66 20 0.14
67 77 0.53
68 1 0.01
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.45
Consensus pattern (65 bp):
TTTCTTTTGGAAAAAAATCTTTGAATATGTTTCTTTGAAACAAAATTTTGTCTCTCTTAAGATAA
Found at i:327407 original size:36 final size:35
Alignment explanation
Indices: 327354--327467 Score: 109
Period size: 36 Copynumber: 3.4 Consensus size: 35
327344 GAAACACTGA
*
327354 TCTTTGAGATCA-ATTCCCTTTAAACGAATTTTGTC
1 TCTTTGAGA-CAGTTTCCCTTTAAACGAATTTTGTC
*
327389 TCATTTGAGACAGTTTCCCTTTAAACG----TCG--
1 TC-TTTGAGACAGTTTCCCTTTAAACGAATTTTGTC
* *
327419 TCTTTGAGTC-GTTTCCCTTAAAACGAATTTTGTC
1 TCTTTGAGACAGTTTCCCTTTAAACGAATTTTGTC
327453 TCTTTTGAGACAGTT
1 TC-TTTGAGACAGTT
327468 GCTTTTAAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 19
0.72 0.07 0.22
Matches are distributed among these distances:
28 14 0.22
29 7 0.11
30 2 0.03
32 4 0.06
34 2 0.03
35 11 0.17
36 23 0.37
ACGTcount: A:0.23, C:0.20, G:0.15, T:0.42
Consensus pattern (35 bp):
TCTTTGAGACAGTTTCCCTTTAAACGAATTTTGTC
Found at i:327554 original size:28 final size:28
Alignment explanation
Indices: 327483--327564 Score: 94
Period size: 28 Copynumber: 2.9 Consensus size: 28
327473 TAAAAATATC
* * *
327483 ATCTTTGAGTTTATTTTTCTTGAAACAA
1 ATCTTTGAATTTGTTTCTCTTGAAACAA
** *
327511 ATCTTTGGGTTTGTTTCTTTTGAAACAA
1 ATCTTTGAATTTGTTTCTCTTGAAACAA
327539 ATCTTT-AATTTGGTTTCTCTTGAAAC
1 ATCTTTGAATTT-GTTTCTCTTGAAAC
327565 CATAACTCCT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
27 3 0.07
28 43 0.93
ACGTcount: A:0.24, C:0.12, G:0.13, T:0.50
Consensus pattern (28 bp):
ATCTTTGAATTTGTTTCTCTTGAAACAA
Found at i:327680 original size:43 final size:44
Alignment explanation
Indices: 327622--327809 Score: 138
Period size: 43 Copynumber: 4.3 Consensus size: 44
327612 TCATCCCCAG
* * *
327622 ACCAGATCTCTTCATCACGTATGAGCCGTGTCA-ACCATAGATA
1 ACCAGACCTCCTCATCACGTATGAGCCGTGTCATACCCTAGATA
* * * * *
327665 ACCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATG
1 ACCAGACC-TCCTCATCACGTATGAGCCGTGTCAT-ACC-CTAGATA
* * * * *
327711 GCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCAG---
1 ACCAGACCTCCTCATCACGTATGAGCCGTGTCATACCCTAGATA
* * * *
327752 ACCAGATCTCCTCATCGCGTAAGAGCCGTGTCA-CCCCTAGATA
1 ACCAGACCTCCTCATCACGTATGAGCCGTGTCATACCCTAGATA
327795 ACCAG-CCGTCCTCAT
1 ACCAGACC-TCCTCAT
327810 TGCGTAGGAA
Statistics
Matches: 112, Mismatches: 24, Indels: 18
0.73 0.16 0.12
Matches are distributed among these distances:
40 5 0.04
41 28 0.25
42 2 0.02
43 38 0.34
44 2 0.02
45 5 0.04
46 31 0.28
47 1 0.01
ACGTcount: A:0.25, C:0.33, G:0.18, T:0.24
Consensus pattern (44 bp):
ACCAGACCTCCTCATCACGTATGAGCCGTGTCATACCCTAGATA
Found at i:327736 original size:89 final size:83
Alignment explanation
Indices: 327583--327743 Score: 223
Period size: 83 Copynumber: 1.9 Consensus size: 83
327573 CTAAAGATGG
* * *
327583 CCAGCCGTCCTTATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCTTCATCACGTATGAGC
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGAACTCTTCATCACGTATGAGC
327648 CGTGTCAACCATAGATAA
66 CGTGTCAACCATAGATAA
* *
327666 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTCATC-CC--CAGA---CCAGAACTCTTCATCACGT
327731 ATGAGCCGTGTCA
60 ATGAGCCGTGTCA
327744 TTCCCCAGAC
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
83 31 0.46
84 2 0.03
86 3 0.04
89 31 0.46
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (83 bp):
CCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGAACTCTTCATCACGTATGAGC
CGTGTCAACCATAGATAA
Found at i:327809 original size:130 final size:133
Alignment explanation
Indices: 327607--327927 Score: 445
Period size: 130 Copynumber: 2.4 Consensus size: 133
327597 CATGTAGGAA
* * *
327607 CCGTGTCATCCCCAGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCC
1 CCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAAGAGCCGTGTCACCCATAGATAACCAGCC
*
327672 GTCCTCATCACGTAGGAACCGTGTTATCACC-TT-T-AGATGGCC-AGAACTCTTCATCACGTAT
66 GTCCTCATCACGTAGGAACCGAGTTATCACCTTTCTAAGATGGCCAAGAACTCTTCATCACGTAT
327733 GAG
131 GAG
* *
327736 CCGTGTCATTCCCCAGACCAGATCTCCTCATCGCGTAAGAGCCGTGTCACCCCTAGATAACCAGC
1 CCGTGTCA-TCCCCAGACCAGATCTCCTCATCACGTAAGAGCCGTGTCACCCATAGATAACCAGC
**
327801 CGTCCTCATTGCGTAGGAACCGAGTTATCACCTTTCCTAAAGATGGCCAAGAACTCTTCATCACG
65 CGTCCTCATCACGTAGGAACCGAGTTATCACCTTT-CT-AAGATGGCCAAGAACTCTTCATCACG
327866 TATGAG
128 TATGAG
** * * * *
327872 AAGTGTCATCCCTC-GACCATATTTCCTCATCACGTAGGAGCCGTGTCACCCTTAGA
1 CCGTGTCATCCC-CAGACCAGATCTCCTCATCACGTAAGAGCCGTGTCACCCATAGA
327928 CGACCAGACC
Statistics
Matches: 169, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
129 8 0.05
130 80 0.47
131 2 0.01
133 1 0.01
135 49 0.29
136 29 0.17
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.25
Consensus pattern (133 bp):
CCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAAGAGCCGTGTCACCCATAGATAACCAGCC
GTCCTCATCACGTAGGAACCGAGTTATCACCTTTCTAAGATGGCCAAGAACTCTTCATCACGTAT
GAG
Found at i:328129 original size:3 final size:3
Alignment explanation
Indices: 328123--328171 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
328113 TTTTAATATA
** *
328123 TAT TAT TAT TAT TAT CGT TA- TAT TAT TAT TAT TAC TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
328170 TA
1 TA
328172 ATTTACAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:330667 original size:26 final size:27
Alignment explanation
Indices: 330615--330672 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
330605 TAATTCTTTC
*
330615 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCAAAATATTTATATATAC-TATTA
* *
330643 TTTTCATAATATTTATATGTA-TATTA
1 TTTTCAAAATATTTATATATACTATTA
330669 TTTT
1 TTTT
330673 ATTAATGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 9 0.33
28 18 0.67
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (27 bp):
TTTTCAAAATATTTATATATACTATTA
Found at i:335480 original size:7 final size:7
Alignment explanation
Indices: 335463--335504 Score: 57
Period size: 7 Copynumber: 5.7 Consensus size: 7
335453 TATACTCATA
335463 AAAAAAGG
1 AAAAAA-G
335471 AAAAAAG
1 AAAAAAG
*
335478 AAAAAGG
1 AAAAAAG
335485 AAAAAAG
1 AAAAAAG
335492 AAAAAAAG
1 -AAAAAAG
335500 AAAAA
1 AAAAA
335505 TTGAATCAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
7 18 0.58
8 13 0.42
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:335504 original size:14 final size:14
Alignment explanation
Indices: 335464--335496 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
335454 ATACTCATAA
335464 AAAAAGGAAAAAAG
1 AAAAAGGAAAAAAG
335478 AAAAAGGAAAAAAG
1 AAAAAGGAAAAAAG
335492 AAAAA
1 AAAAA
335497 AAGAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (14 bp):
AAAAAGGAAAAAAG
Found at i:338190 original size:24 final size:24
Alignment explanation
Indices: 338163--338219 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
338153 CTCCTTGTCA
338163 GAATCAGAATTCAGGATTTTCTCG
1 GAATCAGAATTCAGGATTTTCTCG
338187 GAATCAGAATTCAGGATTTTCTCG
1 GAATCAGAATTCAGGATTTTCTCG
*
338211 GTATCAGAA
1 GAATCAGAA
338220 GAATTATCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.32
Consensus pattern (24 bp):
GAATCAGAATTCAGGATTTTCTCG
Found at i:340363 original size:22 final size:22
Alignment explanation
Indices: 340336--340399 Score: 119
Period size: 22 Copynumber: 2.9 Consensus size: 22
340326 TACATCTACA
*
340336 CTCTCCAAAGATGATATATTTT
1 CTCTCCAAAGATGATAGATTTT
340358 CTCTCCAAAGATGATAGATTTT
1 CTCTCCAAAGATGATAGATTTT
340380 CTCTCCAAAGATGATAGATT
1 CTCTCCAAAGATGATAGATT
340400 CTCTTTTTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (22 bp):
CTCTCCAAAGATGATAGATTTT
Found at i:341163 original size:20 final size:20
Alignment explanation
Indices: 341102--341164 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 20
341092 TTTCCAGAAG
341102 TGTTCATAATGAGAAGAACT
1 TGTTCATAATGAGAAGAACT
** ** * *
341122 CATGAAGAAGGAGAAGAA--
1 TGTTCATAATGAGAAGAACT
341140 -GTTCATAATGAGAAGAACT
1 TGTTCATAATGAGAAGAACT
341159 TGTTCA
1 TGTTCA
341165 ACCTTGCCTT
Statistics
Matches: 29, Mismatches: 11, Indels: 6
0.63 0.24 0.13
Matches are distributed among these distances:
17 12 0.41
20 17 0.59
ACGTcount: A:0.43, C:0.10, G:0.24, T:0.24
Consensus pattern (20 bp):
TGTTCATAATGAGAAGAACT
Found at i:342002 original size:26 final size:27
Alignment explanation
Indices: 341966--342016 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
341956 AGCAAAGGTT
* *
341966 CTTTACATTTTGTTTTTAT-TTTTTAG
1 CTTTACATTTTATTATTATCTTTTTAG
341992 CTTTACATTTTATTATTATCTTTTT
1 CTTTACATTTTATTATTATCTTTTT
342017 TTCGAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.18, C:0.10, G:0.04, T:0.69
Consensus pattern (27 bp):
CTTTACATTTTATTATTATCTTTTTAG
Found at i:342812 original size:136 final size:138
Alignment explanation
Indices: 342565--342838 Score: 500
Period size: 136 Copynumber: 2.0 Consensus size: 138
342555 TCACACTCAG
*
342565 GTCACTAGACTTTTAGAGTTTTTTAAATTTAAATCACTATTTCATGGGTTAATCATCTATAAATC
1 GTCACTAGACTTTGAGAGTTTTTTAAATTTAAATCACTATTTCATGGGTTAA-CATCTATAAATC
342630 CTCCTAGTTTAGGCATTTTTTTAGTTTGGTCACTGATATCCTTTATTTTTATATTTTT-AATTTG
65 CTCCTAGTTTAGGCATTTTTTTAGTTTGGTCACTGATATCCTTTATTTTTATATTTTTGAA-TTG
342694 AGCATACTAT
129 AGCATACTAT
342704 GTCACTAGACTTTGAGAGTTTTTTAAATTTAAATCACTATTTCATGGGTT-A-ATCTATAAATCC
1 GTCACTAGACTTTGAGAGTTTTTTAAATTTAAATCACTATTTCATGGGTTAACATCTATAAATCC
342767 TCCTAGTTTAGGCATTTTTTTAGTTTGGTCACTGATATCCTTTATTTTTATATTTTTGAATTGAG
66 TCCTAGTTTAGGCATTTTTTTAGTTTGGTCACTGATATCCTTTATTTTTATATTTTTGAATTGAG
342832 CATACTA
131 CATACTA
342839 ATTTTATTTT
Statistics
Matches: 133, Mismatches: 1, Indels: 5
0.96 0.01 0.04
Matches are distributed among these distances:
136 81 0.61
137 2 0.02
138 1 0.01
139 49 0.37
ACGTcount: A:0.27, C:0.14, G:0.12, T:0.47
Consensus pattern (138 bp):
GTCACTAGACTTTGAGAGTTTTTTAAATTTAAATCACTATTTCATGGGTTAACATCTATAAATCC
TCCTAGTTTAGGCATTTTTTTAGTTTGGTCACTGATATCCTTTATTTTTATATTTTTGAATTGAG
CATACTAT
Found at i:345855 original size:3 final size:3
Alignment explanation
Indices: 345847--345881 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
345837 TACAAAAGGA
345847 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
345882 ATGAATCACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:349829 original size:225 final size:220
Alignment explanation
Indices: 349313--350107 Score: 947
Period size: 225 Copynumber: 3.6 Consensus size: 220
349303 GATGCTATGA
* * * * *
349313 ACGTGACCTTCAAATCTTCAATCTGACACTCTCCCAATTGAGTTATTCCCGCTTGTTTTCTTAAT
1 ACGTGACCTTCAGATCTTCAATCTGACGCTCTCCCAATTGAGCTATCCCCGCTAGTTTTCTTAAT
* * *
349378 GAACATTTCAATTTAGATCTTCAGTCTGAACTCCATAGATCTTATGCTCTTCAAACTAAGCTTAT
66 GAACATTTCAATTTAGACCTTCAGTCTGAACTCCATAGATCTTGTGCTCTTCACACTAAGCTTAT
* *
349443 C-ATAATATAGTAATTGTTTTTACATTTAAAATAACTAATGAATCAAATTATAATAATAATGCAA
131 CGATAATATAGTAA------TTATATTTAAAATAACTAATG-ATCAAA-CATAATAAT-AT-CAA
* * *
349507 TTCAATTAAAATTAGATGCGACGAACGTGAATTGAAC
186 TTCAATTAAAATTAGATGAG-TGAACGTG-GTTGAAC
* * * *
349544 ACGTGACCTTCA-ATTCTTCAATCTGACGCTCTCCCAATTGAGTTATTCTCGCTTGTTTTCTTAA
1 ACGTGACCTTCAGA-TCTTCAATCTGACGCTCTCCCAATTGAGCTATCCCCGCTAGTTTTCTTAA
* * *
349608 TGAACATTTTAATTTAGACCTTCAGTCTGAACTCTATAGATCTTGTGCTCTTGA-ACTAAGCTTA
65 TGAACATTTCAATTTAGACCTTCAGTCTGAACTCCATAGATCTTGTGCTCTTCACACTAAGCTTA
*
349672 TCGATAATATAGTAATAATATTTAAAATAACTAATGATTCAAACCATAATAATACTCCAATTCAA
130 TCGATAATATAGTAATTATATTTAAAATAACTAATGA-TCAAA-CATAATAATA-T-CAATTCAA
* *
349737 TTAAAACTAGATGTTGTGAACGTGGTTCGAAC
191 TTAAAATTAGATG-AGTGAACGTGGTT-GAAC
* * * *
349769 ACGTAACCTTCAGATCTTCAGTCTGATGCTCTCCCAATTGAGCTATCCCCACTAGTTTTCTTAAT
1 ACGTGACCTTCAGATCTTCAATCTGACGCTCTCCCAATTGAGCTATCCCCGCTAGTTTTCTTAAT
* * * *
349834 GAACATTTCAATTTAGACCTTTAGTCTAAACTCCATAGATCTTGTGCTTTTCACAGTAAGCTTAT
66 GAACATTTCAATTTAGACCTTCAGTCTGAACTCCATAGATCTTGTGCTCTTCACACTAAGCTTAT
*
349899 CGACAATATAGTAATTATATTTAAAATAACTAATG-----AC-T--TAA-ATC-A-T-AA-TAAA
131 CGATAATATAGTAATTATATTTAAAATAACTAATGATCAAACATAATAATATCAATTCAATTAAA
* *
349951 ATTAGATACAGTGAACATGGATTGAAC
196 ATTAGAT-GAGTGAACGTGG-TTGAAC
* *
349978 ACGTGACCTTCAGATCTTCAGTCTGACGCTCTCCCAACTGAGCTATCCCCGCTAGTTTTCTTAAT
1 ACGTGACCTTCAGATCTTCAATCTGACGCTCTCCCAATTGAGCTATCCCCGCTAGTTTTCTTAAT
* *
350043 GAACATTTCAATTTAGACCTTCACTCTGAACTCCATAGATCTTGTGCTCTTCAGACTAAGCTTAT
66 GAACATTTCAATTTAGACCTTCAGTCTGAACTCCATAGATCTTGTGCTCTTCACACTAAGCTTAT
350108 GTGGATCAAA
Statistics
Matches: 507, Mismatches: 47, Indels: 42
0.85 0.08 0.07
Matches are distributed among these distances:
209 143 0.28
210 4 0.01
211 1 0.00
212 1 0.00
213 1 0.00
214 1 0.00
215 1 0.00
216 3 0.01
218 1 0.00
219 1 0.00
220 1 0.00
224 4 0.01
225 166 0.33
226 45 0.09
230 13 0.03
231 121 0.24
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.35
Consensus pattern (220 bp):
ACGTGACCTTCAGATCTTCAATCTGACGCTCTCCCAATTGAGCTATCCCCGCTAGTTTTCTTAAT
GAACATTTCAATTTAGACCTTCAGTCTGAACTCCATAGATCTTGTGCTCTTCACACTAAGCTTAT
CGATAATATAGTAATTATATTTAAAATAACTAATGATCAAACATAATAATATCAATTCAATTAAA
ATTAGATGAGTGAACGTGGTTGAAC
Found at i:350229 original size:141 final size:141
Alignment explanation
Indices: 349982--350248 Score: 408
Period size: 141 Copynumber: 1.9 Consensus size: 141
349972 TTGAACACGT
* *
349982 GACCTTCAGATCTTCAGTCTGACGCTCTCCCAACTGAGCTATCCCCGCTAGTTTTCTTAATGAAC
1 GACCTTCAAATCTTAAGTCTGACGCTCTCCCAACTGAGCTATCCCCGCTAGTTTTCTTAATGAAC
* * * *
350047 ATTTCAATTTAGACCTTCACTCTGAACTCCATAGATCTTGTGCTCTTCAGACTAAGCTTATGTGG
66 ATTTCAATTTAGACATTCACACTGAACTCCATAGATCTTGTGATCTTCAAACTAAGCTTATGTGG
350112 ATCAAACATGG
131 ATCAAACATGG
* *
350123 GACCTTCAAATCTTAAGTCTGATGCTCTCCCAACTGAGCTATCCCCGCTTGTTTTCTTAATGAAC
1 GACCTTCAAATCTTAAGTCTGACGCTCTCCCAACTGAGCTATCCCCGCTAGTTTTCTTAATGAAC
* * * * * *
350188 ATTTCCATTTAGATATTCAGACTGAACTCCATATATTTTGTGATCTTTAAACTAAGCTTAT
66 ATTTCAATTTAGACATTCACACTGAACTCCATAGATCTTGTGATCTTCAAACTAAGCTTAT
350249 CGATTATAAT
Statistics
Matches: 112, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
141 112 1.00
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (141 bp):
GACCTTCAAATCTTAAGTCTGACGCTCTCCCAACTGAGCTATCCCCGCTAGTTTTCTTAATGAAC
ATTTCAATTTAGACATTCACACTGAACTCCATAGATCTTGTGATCTTCAAACTAAGCTTATGTGG
ATCAAACATGG
Found at i:350284 original size:13 final size:13
Alignment explanation
Indices: 350266--350291 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
350256 AATATACTCC
350266 AATTCAATTTTAA
1 AATTCAATTTTAA
350279 AATTCAATTTTAA
1 AATTCAATTTTAA
350292 TTAAATGCAG
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:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
AATTCAATTTTAA
Found at i:351542 original size:138 final size:140
Alignment explanation
Indices: 351272--351548 Score: 366
Period size: 138 Copynumber: 2.0 Consensus size: 140
351262 GCGGTGAACA
* *
351272 TGGATCGAACACGTGACCTTCAGATCTTCAATCTGACGCTCTCCCAACTGAGCTATCCCGCTAGT
1 TGGATCGAACACGTGACCTTCAAATATTCAATCTGACGCTCTCCCAACTGAGCTATCCCGCTAGT
* * * *
351337 TTTCTTAATGAACATTTCAATTTAGACCTTCACTCTGAACTCCATAGATCTTGTGCTCTTCAGAC
66 TTTCTTAATGAACATTTCAATTTAGACATTCAATCTGAACTCCATAGATCTTGTGATCTTCAAAC
*
351402 TAAGTTTATG
131 TAAGCTTATG
* * * *
351412 TGGATC-AACATGTGACCTTCAAATATT-AAGTTTGATGCTCT-CCAACTGAGCTATCCCCGCTT
1 TGGATCGAACACGTGACCTTCAAATATTCAA-TCTGACGCTCTCCCAACTGAGCTAT-CCCGCTA
* * *
351474 G-TTTCTTAATGAACATTTCAATTTAGATATTCAAAT-TGAACTCCATATATCTTGTGATCTTTA
64 GTTTTCTTAATGAACATTTCAATTTAGACATTC-AATCTGAACTCCATAGATCTTGTGATCTTCA
351537 AACTAAGCTTAT
128 AACTAAGCTTAT
351549 CAAATTATAA
Statistics
Matches: 120, Mismatches: 14, Indels: 8
0.85 0.10 0.06
Matches are distributed among these distances:
138 78 0.65
139 36 0.30
140 6 0.05
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (140 bp):
TGGATCGAACACGTGACCTTCAAATATTCAATCTGACGCTCTCCCAACTGAGCTATCCCGCTAGT
TTTCTTAATGAACATTTCAATTTAGACATTCAATCTGAACTCCATAGATCTTGTGATCTTCAAAC
TAAGCTTATG
Found at i:354198 original size:24 final size:25
Alignment explanation
Indices: 354171--354240 Score: 65
Period size: 26 Copynumber: 2.8 Consensus size: 25
354161 AATAGTAAGT
354171 AAAAAACAAATAATAATATATATAAA-
1 AAAAAACAAATAATAATA-A-ATAAAC
* *
354197 AAAGAA-AAAGAA-AATAAATAAAC
1 AAAAAACAAATAATAATAAATAAAC
354220 AAATAAACAAAATAATAATAA
1 AAA-AAAC-AAATAATAATAA
354241 CAAGTACGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
22 5 0.14
23 4 0.11
24 6 0.17
25 5 0.14
26 10 0.29
27 5 0.14
ACGTcount: A:0.76, C:0.04, G:0.03, T:0.17
Consensus pattern (25 bp):
AAAAAACAAATAATAATAAATAAAC
Found at i:354260 original size:2 final size:2
Alignment explanation
Indices: 354253--354304 Score: 74
Period size: 2 Copynumber: 27.5 Consensus size: 2
354243 AGTACGAATA
*
354253 AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT A- AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
354293 AT A- AT AT AT AT A
1 AT AT AT AT AT AT A
354305 AATTAATAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
1 3 0.07
2 43 0.93
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:354932 original size:6 final size:5
Alignment explanation
Indices: 354834--355004 Score: 72
Period size: 6 Copynumber: 33.2 Consensus size: 5
354824 AAAATAAAAA
* *
354834 AATAT AATAT AATAA AATAT AA-A- AATAT ACATAT ATATAT AA-AT AAGTAG
1 AATAT AATAT AATAT AATAT AATAT AATAT A-ATAT A-ATAT AATAT AA-TAT
* * *
354884 AATAA AAGGAA AATAT AATAGT AA-A- AATAAT AATA- AATAT AATACT
1 AATAT AA-TAT AATAT AATA-T AATAT AAT-AT AATAT AATAT AATA-T
* * *
354930 AATAAT AA-A- AAAAT AATAT AATAT ATTAT ATATAT ATTAT -ATAT ATATAT
1 AAT-AT AATAT AATAT AATAT AATAT AATAT A-ATAT AATAT AATAT A-ATAT
*
354980 ATATAT CTATAT ATATAT ATATAT A
1 A-ATAT -AATAT A-ATAT A-ATAT A
355005 TGGGTAATAA
Statistics
Matches: 131, Mismatches: 15, Indels: 39
0.71 0.08 0.21
Matches are distributed among these distances:
3 6 0.05
4 15 0.11
5 50 0.38
6 59 0.45
7 1 0.01
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.36
Consensus pattern (5 bp):
AATAT
Found at i:355022 original size:2 final size:2
Alignment explanation
Indices: 354945--355005 Score: 92
Period size: 2 Copynumber: 32.0 Consensus size: 2
354935 TAAAAAAATA
354945 AT AT A- AT AT AT -T AT AT AT AT AT -T AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
354984 AT CT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
355006 GGGTAATAAC
Statistics
Matches: 54, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
1 3 0.06
2 51 0.94
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:357232 original size:56 final size:57
Alignment explanation
Indices: 357146--357252 Score: 132
Period size: 56 Copynumber: 1.9 Consensus size: 57
357136 AATTAAAATG
* *
357146 AAAAGAAAACAAATTAAGTAAAATGATAAAATGAAGAAAGCAAAA-AAAATAGTAAGT
1 AAAAGAAAACAAATTAAGTAAAATGATAAAAAGAA-AAAGAAAAAGAAAATAGTAAGT
*
357203 AAAA-AAAACAAA-TAA-TAAAATATATTAAAAAGAAAAAGAAAAAGAAAATA
1 AAAAGAAAACAAATTAAGTAAAAT-GA-TAAAAAGAAAAAGAAAAAGAAAATA
357253 AATAAAACAA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
54 6 0.14
55 12 0.27
56 22 0.50
57 4 0.09
ACGTcount: A:0.72, C:0.03, G:0.10, T:0.15
Consensus pattern (57 bp):
AAAAGAAAACAAATTAAGTAAAATGATAAAAAGAAAAAGAAAAAGAAAATAGTAAGT
Found at i:357407 original size:2 final size:2
Alignment explanation
Indices: 357402--357465 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
357392 AGATAATTAC
357402 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
357444 AT AT -T AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
357466 GTAACAATAC
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 60 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:357868 original size:12 final size:11
Alignment explanation
Indices: 357840--357885 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
357830 ATAACAAAAT
* *
357840 AATAATATAAA
1 AATAATACAAG
357851 AATAATACAAG
1 AATAATACAAG
357862 TAATAATACAAG
1 -AATAATACAAG
357874 AATAATA-AAG
1 AATAATACAAG
357884 AA
1 AA
357886 GAGAAAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
10 5 0.16
11 16 0.50
12 11 0.34
ACGTcount: A:0.67, C:0.04, G:0.07, T:0.22
Consensus pattern (11 bp):
AATAATACAAG
Found at i:357989 original size:9 final size:10
Alignment explanation
Indices: 357836--358000 Score: 53
Period size: 9 Copynumber: 16.3 Consensus size: 10
357826 ATATATAACA
357836 AAATAATAAT
1 AAATAATAAT
*
357846 ATAAAAATAAT
1 A-AATAATAAT
357857 ACAAGTAATAAT
1 A-AA-TAATAAT
*
357869 ACAAGAATAAT
1 A-AATAATAAT
* *
357880 AAAGAAGAGA-
1 AAATAATA-AT
357890 AAATAA-AA-
1 AAATAATAAT
357898 AATATAATAAT
1 AA-ATAATAAT
*
357909 -AATAAATAAA
1 AAAT-AATAAT
*
357919 AAATAA-CAT
1 AAATAATAAT
*
357928 ATATAAT-AT
1 AAATAATAAT
357937 AAATAAGTAGAAT
1 AAATAA-T--AAT
*
357950 AAA-AGGAAAAT
1 AAATA--ATAAT
* *
357961 ATATAGTAA-
1 AAATAATAAT
357970 AAATAATAAT
1 AAATAATAAT
357980 AAAT-ATAAT
1 AAATAATAAT
*
357989 -AGTAATAAT
1 AAATAATAAT
357998 AAA
1 AAA
358001 AATGCAAAGA
Statistics
Matches: 117, Mismatches: 19, Indels: 38
0.67 0.11 0.22
Matches are distributed among these distances:
8 5 0.04
9 37 0.32
10 30 0.26
11 27 0.23
12 12 0.10
13 5 0.04
14 1 0.01
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.24
Consensus pattern (10 bp):
AAATAATAAT
Found at i:358592 original size:37 final size:37
Alignment explanation
Indices: 358551--358647 Score: 131
Period size: 37 Copynumber: 2.6 Consensus size: 37
358541 GGATCCTATC
* *
358551 TTTAGGAGTTTAAATCATAGTAGAACTCTATCATATT
1 TTTAGGAGTTTGAATCCTAGTAGAACTCTATCATATT
* * * *
358588 TTTAGGAGTTTGAATCCTAGCAAAATTCTATCCTATT
1 TTTAGGAGTTTGAATCCTAGTAGAACTCTATCATATT
*
358625 TTTAGGAATTTGAATCCTAGTAG
1 TTTAGGAGTTTGAATCCTAGTAG
358648 GACGAAAAGG
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.40
Consensus pattern (37 bp):
TTTAGGAGTTTGAATCCTAGTAGAACTCTATCATATT
Found at i:359516 original size:106 final size:106
Alignment explanation
Indices: 359378--360356 Score: 1342
Period size: 106 Copynumber: 9.3 Consensus size: 106
359368 GCATTGTTCC
* * ** * * *
359378 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCGTGAAATTATTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* * * * *
359442 ACCTGCCGTCCCTTCGTTGTGAAGTTGAAATTGTG-TGTTCCT-
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG-T-CTG
* * *
359484 GAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGACTCT-AAA-T--GAA-AT-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * * *
359543 TCAGCCG-CCCTTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTT
66 CCAGCGGTCCC-TTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * *
359585 G-GTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
359649 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
359690 GAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGATAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
359755 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
359796 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
359861 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
359902 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTATG--GACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTT-TGTTGACA
* *
359965 ACCAGTGGTCCC-TCGTTC-TGAAGTTGAACTTGCGTTGTCTT
65 ACCAGCGGTCCCTTCG-TCGTGAAGTTGAACTTGCGTTGTCTG
* *
360006 GAGTCCAATATTCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
360071 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
360112 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATAT-ACTTTGAAATTGAGAAGTTGTTTGTTGATA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAAT-TGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
*
360176 ACCAGCGGTCCCTTTGTCGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * *
360218 GAGTCCAATATCCTTCATTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
360283 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
360324 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
360357 TACTCTCGAG
Statistics
Matches: 787, Mismatches: 65, Indels: 42
0.88 0.07 0.05
Matches are distributed among these distances:
99 4 0.01
100 71 0.09
101 7 0.01
102 4 0.01
103 2 0.00
104 81 0.10
105 41 0.05
106 570 0.72
107 7 0.01
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:360156 original size:422 final size:417
Alignment explanation
Indices: 359378--360362 Score: 1442
Period size: 422 Copynumber: 2.3 Consensus size: 417
359368 GCATTGTTCC
* * * ** * * *
359378 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGTGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* * * *
359443 CCTGCCGTCCCTTCGTTGTGAAGTTGAAATTGTG-TGTTCCT-GAGTCCAATATCCTTCGCTGTG
66 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTG-T-CTGGAGTCCAATATCCTTCGCTGTG
* * * * *
359506 AAGTTAAAATTGACTCTAAATGAAATTTTGTTGACAATCAGCCGCCCTTTCGTCGTGAAGTTGAG
129 AAGTTGAAATTGACTCTAAATGAAATTTTATGGACAACCAGCCGCCC-TTCGTCGTGAAGTTGAA
* *
359571 CTTGTGTTGTCTTTGGTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGT
193 CTTGCGTTGTCTTTGGTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAAT
*
359636 TGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATAT
258 TGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* *
359701 CCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGATAACCAGCGGTCCC
323 CCTACGCTGTGAAGTTGAAATTGACTCTGAAATTGAGAAATTGTTTATTGATAACCAGCGGTCCC
359766 TTCGTCGTGAAGTTGAACTTGCATTGTCTG
388 TTCGTCGTGAAGTTGAACTTGCATTGTCTG
*
359796 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
359861 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
66 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
* * **
359926 GTTGAAATTGGCTCTGAAATTGGGAAGTTATTATGGACAACCAGTGGTCCC-TCGTTC-TGAAGT
131 GTTGAAATTGACTCT-AAA-T--GAAATT-TTATGGACAACCAGCCG-CCCTTCG-TCGTGAAGT
* * *
359989 TGAACTTGCGTTGTC-TTGAGTCCAATATTCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGG
189 TGAACTTGCGTTGTCTTTG-GTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGG
*
360053 GAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
253 GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
* * * * *
360118 AATATCCTTCGTTGTGAAGTTGAAATAT-ACTTTGAAATTGAGAAGTTGTTTGTTGATAACCAGC
318 AATATCCTACGCTGTGAAGTTGAAAT-TGACTCTGAAATTGAGAAATTGTTTATTGATAACCAGC
* *
360182 GGTCCCTTTGTCGTGAAGTTGAACTTGCGTTGTCTG
382 GGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
* *
360218 GAGTCCAATATCCTTCATTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
360283 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
66 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
*
360348 GTTGAAATTTACTCT
131 GTTGAAATTGACTCT
360363 CGAGCAAATT
Statistics
Matches: 511, Mismatches: 45, Indels: 18
0.89 0.08 0.03
Matches are distributed among these distances:
417 2 0.00
418 123 0.24
419 5 0.01
420 1 0.00
421 3 0.01
422 359 0.70
423 15 0.03
424 3 0.01
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (417 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
GTTGAAATTGACTCTAAATGAAATTTTATGGACAACCAGCCGCCCTTCGTCGTGAAGTTGAACTT
GCGTTGTCTTTGGTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGT
TTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCT
ACGCTGTGAAGTTGAAATTGACTCTGAAATTGAGAAATTGTTTATTGATAACCAGCGGTCCCTTC
GTCGTGAAGTTGAACTTGCATTGTCTG
Found at i:361126 original size:22 final size:22
Alignment explanation
Indices: 361100--361176 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
361090 TTATGTTTGG
361100 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
361122 TCAAAGGCTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
361144 TCATAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
361166 TCAACGGTTTG
1 TCAAAGGTTTG
361177 ATAGGGTAGC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.21, C:0.16, G:0.27, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:365838 original size:58 final size:57
Alignment explanation
Indices: 365750--365858 Score: 134
Period size: 56 Copynumber: 1.9 Consensus size: 57
365740 AATTAAAATG
* *
365750 AAAAGAAAACAAATTAAGTAAAATGATAAAATGAAGAAAGCAAAAATAAAATAGTAAGT
1 AAAAGAAAACAAATTAAGTAAAATGATAAAAAGAA-AAAG-AAAAAGAAAATAGTAAGT
*
365809 AAAA-AAAACAAA-TAA-TAAAATATATTAAAAAGAAAAAGAAAAAGAAAATA
1 AAAAGAAAACAAATTAAGTAAAAT-GA-TAAAAAGAAAAAGAAAAAGAAAATA
365859 AATAAAACAA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
56 17 0.38
57 8 0.18
58 16 0.36
59 4 0.09
ACGTcount: A:0.72, C:0.03, G:0.10, T:0.16
Consensus pattern (57 bp):
AAAAGAAAACAAATTAAGTAAAATGATAAAAAGAAAAAGAAAAAGAAAATAGTAAGT
Found at i:365844 original size:28 final size:27
Alignment explanation
Indices: 365750--365884 Score: 73
Period size: 28 Copynumber: 4.7 Consensus size: 27
365740 AATTAAAATG
365750 AAAAGAAAACAAATTAAGTAAAATGATA-A
1 AAAAGAAAACAAA-TAA-TAAAAT-ATATA
*
365779 AATGAAGAAAGCAAA-AATAAAATAGTA-A
1 AA--AAGAAAACAAATAATAAAATA-TATA
365807 GTAAAA-AAAACAAATAATAAAATATATTA
1 --AAAAGAAAACAAATAATAAAATATA-TA
* * *
365836 AAAAGAAAA-AGAAAAAGAAAATAAATA
1 AAAAGAAAACA-AATAATAAAATATATA
*
365863 AAACAAATAAACAAAATAATAA
1 AAA-AGA-AAAC-AAATAATAA
365885 TAACAAAGTA
Statistics
Matches: 84, Mismatches: 8, Indels: 27
0.71 0.07 0.23
Matches are distributed among these distances:
27 20 0.24
28 37 0.44
29 8 0.10
30 8 0.10
31 11 0.13
ACGTcount: A:0.73, C:0.04, G:0.08, T:0.16
Consensus pattern (27 bp):
AAAAGAAAACAAATAATAAAATATATA
Found at i:365925 original size:32 final size:29
Alignment explanation
Indices: 365878--365945 Score: 77
Period size: 32 Copynumber: 2.3 Consensus size: 29
365868 AATAAACAAA
* *
365878 ATAAT-AATAACAAAGTACGAATAATATATAT
1 ATAATAAATAAAAAAGTA--AAT-ATATAAAT
365909 ATAATAAATAAAAAAGTAAATATATAAAT
1 ATAATAAATAAAAAAGTAAATATATAAAT
365938 -TAATAAAT
1 ATAATAAAT
365946 TAAATGATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 8 0.24
29 7 0.21
30 3 0.09
31 5 0.15
32 11 0.32
ACGTcount: A:0.63, C:0.03, G:0.04, T:0.29
Consensus pattern (29 bp):
ATAATAAATAAAAAAGTAAATATATAAAT
Found at i:366008 original size:2 final size:2
Alignment explanation
Indices: 366001--366031 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
365991 GATAATTACA
366001 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
366032 GTAACAATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:366477 original size:23 final size:26
Alignment explanation
Indices: 366452--366508 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
366442 AAGAAAGAGA
*
366452 AAATAAAAAATATA-ATA-ATAATAA
1 AAATAAAAAATAAACATATATAATAA
*
366476 AATATAAAAAATAAACATATATAATAT
1 AA-ATAAAAAATAAACATATATAATAA
366503 AAATAA
1 AAATAA
366509 GTAGAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 2 0.07
25 11 0.39
26 7 0.25
27 8 0.29
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (26 bp):
AAATAAAAAATAAACATATATAATAA
Found at i:366544 original size:12 final size:12
Alignment explanation
Indices: 366522--366566 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
366512 GAATAAAAGG
366522 AAAATATAATAGT
1 AAAA-ATAATAGT
*
366535 AAAAATAATAAT
1 AAAAATAATAGT
*
366547 AAATATAATAGT
1 AAAAATAATAGT
*
366559 AATAATAA
1 AAAAATAA
366567 AAATGCAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 23 0.85
13 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (12 bp):
AAAAATAATAGT
Found at i:366556 original size:15 final size:15
Alignment explanation
Indices: 366453--366507 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
366443 AGAAAGAGAA
*
366453 AATAAAAAATATAAT
1 AATAATAAATATAAT
366468 AATAATAAAATATAA-
1 AATAAT-AAATATAAT
*
366483 AA-AATAAACATATAT
1 AATAATAAATATA-AT
366498 AAT-ATAAATA
1 AATAATAAATA
366508 AGTAGAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
13 6 0.18
14 4 0.12
15 15 0.45
16 8 0.24
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (15 bp):
AATAATAAATATAAT
Found at i:367168 original size:37 final size:37
Alignment explanation
Indices: 367127--367223 Score: 140
Period size: 37 Copynumber: 2.6 Consensus size: 37
367117 GGATCCTATC
*
367127 TTTAGGAGTTTAAATCATAGTAGAACTCTATCATATT
1 TTTAGGAGTTTAAATCCTAGTAGAACTCTATCATATT
* * * *
367164 TTTAGGAGTTTGAATCCTAGCAAAATTCTATCATATT
1 TTTAGGAGTTTAAATCCTAGTAGAACTCTATCATATT
*
367201 TTTAGGAATTTAAATCCTAGTAG
1 TTTAGGAGTTTAAATCCTAGTAG
367224 GATGAAAAGG
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.40
Consensus pattern (37 bp):
TTTAGGAGTTTAAATCCTAGTAGAACTCTATCATATT
Found at i:368272 original size:106 final size:106
Alignment explanation
Indices: 367953--368934 Score: 1383
Period size: 106 Copynumber: 9.3 Consensus size: 106
367943 AGTATTGTTC
* * ** * * *
367953 TGAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCGTGAAATTATTTGTTGAC
1 TGAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGAC
* * * * *
368017 AACCAGCCGTCCCTACGTTGTGAAGTTGAACTTGTGTTGTCC
65 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * *
368059 TGAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGACTCTG-AA-T--GAA-AT-TTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* * * * *
368118 ATCAGCCG-CCCTTTCGTCGTGAAGTTGAGCTTGTGTTATCT
66 ACCAGCGGTCCC-TTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * *
368159 TGGGTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
368224 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * *
368265 TGAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
368330 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * *
368371 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
368436 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * *
368477 GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTATGGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
*
368542 ACCAGTGGTCCCTTCGTTC-TGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCG-TCGTGAAGTTGAACTTGCGTTGTCT
* *
368583 TGAGTCCAATATTCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
368648 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT-T
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * * *
368688 TGGAGTCCAATATCCTTCGTTGTGAAGTTAAAATAT-ACTTTGAAATTGAGAAGTTGTTTGTTGA
1 T-GAGTCCAATATCCTTCGCTGTGAAGTTGAAAT-TGGCTCTGAAATTGGGAAGTTGTTTGTTGA
*
368752 CAACCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
64 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * *
368795 GGAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
*
368860 ACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
*
368901 GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
368935 TACTCTCGAG
Statistics
Matches: 796, Mismatches: 65, Indels: 30
0.89 0.07 0.03
Matches are distributed among these distances:
99 3 0.00
100 76 0.10
101 3 0.00
102 4 0.01
104 3 0.00
105 8 0.01
106 691 0.87
107 8 0.01
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
Found at i:369698 original size:22 final size:22
Alignment explanation
Indices: 369672--369748 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
369662 TTATGTTTGG
369672 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
369694 TCAAAGGCTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
369716 TCATAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
369738 TCAACGGTTTG
1 TCAAAGGTTTG
369749 ATGGGGTAGC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.21, C:0.16, G:0.27, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:370386 original size:15 final size:16
Alignment explanation
Indices: 370366--370399 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
370356 TTCTTTTTGA
370366 TTTTTGTTCT-TTCTT
1 TTTTTGTTCTCTTCTT
*
370381 TTTTTGTTTTCTTCTT
1 TTTTTGTTCTCTTCTT
370397 TTT
1 TTT
370400 AGCTTCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.82
Consensus pattern (16 bp):
TTTTTGTTCTCTTCTT
Found at i:375071 original size:6 final size:6
Alignment explanation
Indices: 375060--375087 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
375050 AATATATTTT
375060 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
375088 TAAATAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:375139 original size:2 final size:2
Alignment explanation
Indices: 375132--375160 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
375122 AGTACGAATA
375132 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
375161 ATAAATAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:375436 original size:2 final size:2
Alignment explanation
Indices: 375429--375467 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
375419 CTTGTGTAGA
375429 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
375468 ATAATAGTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:375710 original size:12 final size:11
Alignment explanation
Indices: 375682--375722 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
375672 TAACAAAATA
* *
375682 AATAATATAAA
1 AATAATACAAG
375693 AATAATACAAG
1 AATAATACAAG
375704 TAATAATACAAG
1 -AATAATACAAG
375716 AATAATA
1 AATAATA
375723 AAAAGAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (11 bp):
AATAATACAAG
Found at i:375944 original size:2 final size:2
Alignment explanation
Indices: 375937--375998 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
375927 AATTAGCAAG
375937 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
375979 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
375999 CTAATTACGG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:393982 original size:3 final size:3
Alignment explanation
Indices: 393974--394005 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
393964 CAAATATTTC
*
393974 TCT TCT TCT TCT TCT TCT TCT TCG TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
394006 CTTTGTGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.34, G:0.03, T:0.62
Consensus pattern (3 bp):
TCT
Found at i:399505 original size:15 final size:15
Alignment explanation
Indices: 399485--399521 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
399475 AACCGATAAG
399485 GAAAGAACTACGGAA
1 GAAAGAACTACGGAA
399500 GAAAGAACTACGGAA
1 GAAAGAACTACGGAA
399515 GAAAGAA
1 GAAAGAA
399522 AAAAAAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.57, C:0.11, G:0.27, T:0.05
Consensus pattern (15 bp):
GAAAGAACTACGGAA
Found at i:402815 original size:3 final size:3
Alignment explanation
Indices: 402807--402857 Score: 59
Period size: 3 Copynumber: 16.3 Consensus size: 3
402797 CCATTTGTAT
*
402807 TAA TAA TAA TAA TAA TAA TAAA TAAA TAA TAA TTAA -AA TAA TAA TAG
1 TAA TAA TAA TAA TAA TAA T-AA T-AA TAA TAA -TAA TAA TAA TAA TAA
402854 TAA T
1 TAA T
402858 GAATTAAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 2 0.05
3 31 0.72
4 10 0.23
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:406965 original size:23 final size:23
Alignment explanation
Indices: 406947--407000 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
406937 GTGTTTGTGT
406947 TGTTCGTTTATGTCCGTTTATTG
1 TGTTCGTTTATGTCCGTTTATTG
* * *
406970 TGTTCGTTTATGTTCATTTATTA
1 TGTTCGTTTATGTCCGTTTATTG
406993 TGTTCGTT
1 TGTTCGTT
407001 CGTTTGTGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.11, C:0.11, G:0.19, T:0.59
Consensus pattern (23 bp):
TGTTCGTTTATGTCCGTTTATTG
Found at i:406983 original size:10 final size:10
Alignment explanation
Indices: 406947--407037 Score: 73
Period size: 10 Copynumber: 9.1 Consensus size: 10
406937 GTGTTTGTGT
406947 TGTTCGTTTA
1 TGTTCGTTTA
*
406957 TGTCCGTTTA
1 TGTTCGTTTA
406967 TTGTGTTCGTTTA
1 ---TGTTCGTTTA
*
406980 TGTTCATTTA
1 TGTTCGTTTA
406990 T-TAT-G-TT-
1 TGT-TCGTTTA
* *
406997 CGTTCGTTTG
1 TGTTCGTTTA
407007 TGTTCGTTTA
1 TGTTCGTTTA
*
407017 CGTTCGTTTA
1 TGTTCGTTTA
407027 TGTTCGTTTA
1 TGTTCGTTTA
407037 T
1 T
407038 CCTTTAAATA
Statistics
Matches: 64, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
7 1 0.02
8 4 0.06
9 3 0.05
10 47 0.73
13 9 0.14
ACGTcount: A:0.10, C:0.12, G:0.20, T:0.58
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:407137 original size:14 final size:15
Alignment explanation
Indices: 407107--407141 Score: 54
Period size: 14 Copynumber: 2.3 Consensus size: 15
407097 AATGTGTTCG
407107 TTTATGTTCGTGTTTA
1 TTTATGTTCG-GTTTA
407123 TTTATGTTC-GTTTA
1 TTTATGTTCGGTTTA
407137 TTTAT
1 TTTAT
407142 TAAATGAACG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.53
16 9 0.47
ACGTcount: A:0.14, C:0.06, G:0.14, T:0.66
Consensus pattern (15 bp):
TTTATGTTCGGTTTA
Found at i:407394 original size:13 final size:13
Alignment explanation
Indices: 407357--407407 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
407347 AATCTTAAAT
*
407357 AATAAATTAAAAA
1 AATAAATTACAAA
*
407370 AATAGAA-AACAAA
1 AATA-AATTACAAA
407383 AATAAATTACAAA
1 AATAAATTACAAA
*
407396 TAAAAAATTACA
1 -AATAAATTACA
407408 TATAACATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
12 2 0.06
13 17 0.55
14 12 0.39
ACGTcount: A:0.73, C:0.06, G:0.02, T:0.20
Consensus pattern (13 bp):
AATAAATTACAAA
Found at i:408967 original size:14 final size:14
Alignment explanation
Indices: 408948--408997 Score: 82
Period size: 14 Copynumber: 3.6 Consensus size: 14
408938 ATTTGTAATT
408948 AACCCTAAGCCTTA
1 AACCCTAAGCCTTA
*
408962 AACCCTAAGCCATA
1 AACCCTAAGCCTTA
*
408976 AACCCTAAACCTTA
1 AACCCTAAGCCTTA
408990 AACCCTAA
1 AACCCTAA
408998 ATCCAATTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.42, C:0.36, G:0.04, T:0.18
Consensus pattern (14 bp):
AACCCTAAGCCTTA
Found at i:408986 original size:7 final size:7
Alignment explanation
Indices: 408948--408998 Score: 57
Period size: 7 Copynumber: 7.3 Consensus size: 7
408938 ATTTGTAATT
408948 AACCCTA
1 AACCCTA
* *
408955 AGCCTTA
1 AACCCTA
408962 AACCCTA
1 AACCCTA
* *
408969 AGCCATA
1 AACCCTA
408976 AACCCTA
1 AACCCTA
*
408983 AACCTTA
1 AACCCTA
408990 AACCCTA
1 AACCCTA
408997 AA
1 AA
408999 TCCAATTATA
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.43, C:0.35, G:0.04, T:0.18
Consensus pattern (7 bp):
AACCCTA
Found at i:410289 original size:31 final size:31
Alignment explanation
Indices: 410253--410313 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
410243 TTATACCATA
* *
410253 AGTCATCCAATTACTAGTAAGATTATAAATG
1 AGTCATCCAATTACTAATAAGATTACAAATG
* *
410284 AGTCATCCAGTTATTAATAAGATTACAAAT
1 AGTCATCCAATTACTAATAAGATTACAAAT
410314 AGGTCACACA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.33
Consensus pattern (31 bp):
AGTCATCCAATTACTAATAAGATTACAAATG
Found at i:416337 original size:34 final size:36
Alignment explanation
Indices: 416293--416394 Score: 163
Period size: 34 Copynumber: 2.9 Consensus size: 36
416283 TTTCGTCCTA
*
416293 CTAGGATTCAAACTCCTAAAAATATGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
*
416328 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
416363 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
416395 GTTCTACTAT
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
34 29 0.48
35 3 0.05
37 29 0.48
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:416418 original size:37 final size:37
Alignment explanation
Indices: 416290--416428 Score: 158
Period size: 37 Copynumber: 3.8 Consensus size: 37
416280 ATTTTTCGTC
* *
416290 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
416327 -T--TAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
416361 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
** * * *
416398 CTACTATTATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
416429 CCACAAGCAC
Statistics
Matches: 88, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
34 31 0.35
35 1 0.01
36 1 0.01
37 55 0.62
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.32
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:416612 original size:21 final size:20
Alignment explanation
Indices: 416585--416682 Score: 88
Period size: 20 Copynumber: 4.8 Consensus size: 20
416575 AATCAGTGTC
416585 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * **
416606 GAAAATCGCAATGCGATAGT
1 CAAAATCGCAACGCGATTTT
* **
416626 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
416646 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
416667 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
416683 ACACATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 31 0.51
21 30 0.49
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:416635 original size:41 final size:41
Alignment explanation
Indices: 416526--416682 Score: 126
Period size: 41 Copynumber: 3.9 Consensus size: 41
416516 AAATGACCAA
* **
416526 CAAAATCGCAACGCGAA-ATAAAAATCGCAACGCGA-TCCC
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
* ** * *
416565 CAGAATCGCAAATC-AGTGTCCAAAATCGCAACGCGATTCTT-
1 CAAAATCGCAACGCGAATAT-CAAAATCGCAACGCGATT-TTC
* * * **
416606 GAAAATCGCAATGCG-ATAGTCAAATTCGCATTGCGATTTTC
1 CAAAATCGCAACGCGAATA-TCAAAATCGCAACGCGATTTTC
*
416647 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGA
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGA
416683 ACACATAAAT
Statistics
Matches: 87, Mismatches: 23, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
38 1 0.01
39 12 0.14
40 17 0.20
41 53 0.61
42 4 0.05
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (41 bp):
CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
Found at i:416692 original size:20 final size:20
Alignment explanation
Indices: 416669--416842 Score: 118
Period size: 20 Copynumber: 8.7 Consensus size: 20
416659 GCGAATATGA
416669 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTAAC-CAT
* * *
416689 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * *
416709 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTAACCAT
****
416729 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTAACCAT
* * *
416749 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * **
416769 ATATCGCAACGCGTATCGGT
1 AAATCGCAACGCGTAACCAT
* *
416789 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGTAA-CCAT
* *
416809 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTAACCAT
416830 AAATCGCAACGCG
1 AAATCGCAACGCG
416843 ATATTTAAAG
Statistics
Matches: 126, Mismatches: 24, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
19 2 0.02
20 107 0.85
21 15 0.12
22 2 0.02
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTAACCAT
Found at i:416713 original size:40 final size:39
Alignment explanation
Indices: 416649--416843 Score: 183
Period size: 40 Copynumber: 4.9 Consensus size: 39
416639 CGATTTTCCA
* ** *
416649 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CAT
* * * *
416689 AAATCGCAATGCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCAT
** * * *
416729 AAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCAT
* * ** *
416769 ATATCGCAACGCGTATCGGTAAATCGCAACGATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAA-CCAT
416809 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
416844 TATTTAAAGC
Statistics
Matches: 127, Mismatches: 25, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
39 1 0.01
40 94 0.74
41 32 0.25
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (39 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACCAT
Found at i:416734 original size:60 final size:60
Alignment explanation
Indices: 416649--416842 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
416639 CGATTTTCCA
* ** * *
416649 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
* * ***
416709 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
* * ** *
416769 ATATCGCAACGCGTATCGGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAATGCGTATCCGT
416830 AAATCGCAACGCG
1 AAATCGCAACGCG
416843 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
Found at i:417264 original size:33 final size:33
Alignment explanation
Indices: 417225--417295 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
417215 TTCACTTAGA
417225 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* * *
417258 TTTCATTTCGCGTTGCTATTCTCTCGTTGTGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
417291 TTTCA
1 TTTCA
417296 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.17, T:0.49
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Done.